PDB Short entry for 2A7B HEADER ENDOCYTOSIS/EXOCYTOSIS 05-JUL-05 2A7B TITLE ON THE ROUTINE USE OF SOFT X-RAYS IN MACROMOLECULAR CRYSTALLOGRAPHY, TITLE 2 PART III- THE OPTIMAL DATA COLLECTION WAVELENGTH COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA-ADAPTIN APPENDAGE DOMAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: AP1G1, ADTG, CLAPG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN TRANSPORT, ENDOCYTOSIS-EXOCYTOSIS COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.MUELLER-DIECKMANN,S.PANJIKAR,P.A.TUCKER,M.S.WEISS REVDAT 4 14-FEB-24 2A7B 1 REMARK SEQADV REVDAT 3 24-FEB-09 2A7B 1 VERSN REVDAT 2 13-SEP-05 2A7B 1 JRNL REVDAT 1 19-JUL-05 2A7B 0 JRNL AUTH C.MUELLER-DIECKMANN,S.PANJIKAR,P.A.TUCKER,M.S.WEISS JRNL TITL ON THE ROUTINE USE OF SOFT X-RAYS IN MACROMOLECULAR JRNL TITL 2 CRYSTALLOGRAPHY. PART III. THE OPTIMAL DATA-COLLECTION JRNL TITL 3 WAVELENGTH. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 61 1263 2005 JRNL REFN ISSN 0907-4449 JRNL PMID 16131760 JRNL DOI 10.1107/S0907444905021475 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 14704 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT : 293 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1015 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 24 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 943 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.40000 REMARK 3 B22 (A**2) : -0.60000 REMARK 3 B33 (A**2) : 0.21000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.095 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.101 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.747 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 966 ; 0.025 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 877 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1315 ; 2.030 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2060 ; 0.877 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 119 ; 6.276 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 41 ;37.094 ;25.854 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 171 ;14.639 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;20.335 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 157 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1049 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 173 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 195 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1078 ; 0.200 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 518 ; 0.200 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 735 ; 0.107 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 82 ; 0.163 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 11 ; 0.838 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 24 ; 0.320 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.218 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 606 ; 1.336 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 237 ; 0.285 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1000 ; 2.726 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 367 ; 5.219 ; 5.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 315 ; 9.071 ;10.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2A7B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000033577. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.80 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14704 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 16.71500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.38500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.88000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.38500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.71500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.88000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 XE XE A 902 O HOH A 50 1.11 REMARK 500 OE1 GLN A 736 OG1 THR A 779 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 795 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 902 DBREF 2A7B A 704 822 UNP P22892 AP1G1_MOUSE 703 821 SEQADV 2A7B MET A 703 UNP P22892 INITIATING METHIONINE SEQRES 1 A 120 MET ILE PRO SER ILE THR ALA TYR SER LYS ASN GLY LEU SEQRES 2 A 120 LYS ILE GLU PHE THR PHE GLU ARG SER ASN THR ASN PRO SEQRES 3 A 120 SER VAL THR VAL ILE THR ILE GLN ALA SER ASN SER THR SEQRES 4 A 120 GLU LEU ASP MET THR ASP PHE VAL PHE GLN ALA ALA VAL SEQRES 5 A 120 PRO LYS THR PHE GLN LEU GLN LEU LEU SER PRO SER SER SEQRES 6 A 120 SER VAL VAL PRO ALA PHE ASN THR GLY THR ILE THR GLN SEQRES 7 A 120 VAL ILE LYS VAL LEU ASN PRO GLN LYS GLN GLN LEU ARG SEQRES 8 A 120 MET ARG ILE LYS LEU THR TYR ASN HIS LYS GLY SER ALA SEQRES 9 A 120 MET GLN ASP LEU ALA GLU VAL ASN ASN PHE PRO PRO GLN SEQRES 10 A 120 SER TRP GLN HET XE A 901 1 HET XE A 902 1 HETNAM XE XENON FORMUL 2 XE 2(XE) FORMUL 4 HOH *87(H2 O) HELIX 1 1 PRO A 771 THR A 775 5 5 HELIX 2 2 PRO A 817 TRP A 821 5 5 SHEET 1 A 5 ILE A 707 LYS A 712 0 SHEET 2 A 5 LEU A 715 ARG A 723 -1 O PHE A 719 N ILE A 707 SHEET 3 A 5 VAL A 730 ASN A 739 -1 O VAL A 732 N GLU A 722 SHEET 4 A 5 ILE A 778 LEU A 785 -1 O GLN A 780 N ILE A 735 SHEET 5 A 5 GLN A 759 LEU A 762 -1 N GLN A 761 O LYS A 783 SHEET 1 B 3 THR A 746 ALA A 753 0 SHEET 2 B 3 MET A 794 HIS A 802 -1 O ASN A 801 N THR A 746 SHEET 3 B 3 SER A 805 VAL A 813 -1 O MET A 807 N TYR A 800 SITE 1 AC1 3 ILE A 735 ILE A 778 GLN A 780 SITE 1 AC2 5 HOH A 50 ASP A 747 ARG A 795 ASN A 801 SITE 2 AC2 5 LEU A 810 CRYST1 33.430 53.760 66.770 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.029913 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018601 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014977 0.00000