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Crystal structure of adenylylsulfate reductase from Desulfovibrio gigas
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JNR PDB ENTRY 1JNR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.4 291 2M ammonium sulfate, 0.1M Tris, 1M guanidine hydrochloride, 0.2M sodium chloride, pH7.4, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.27 62.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 199.629 α = 90 b = 199.629 β = 90 c = 317.422 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2007-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.1 30 92 0.102 0.081 13.63 4.3 132767 122146 3.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.1 3.21 93.9 0.41 0.446 3.64 4.2 12375
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1JNR 3.2 30 5 112993 105084 5561 91.68 0.1949 0.19226 0.1989 0.24497 0.2463 RANDOM 45.365
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.28 0.14 0.28 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.913 r_dihedral_angle_3_deg 18.123 r_dihedral_angle_4_deg 15.58 r_dihedral_angle_1_deg 5.23 r_angle_refined_deg 1.048 r_scangle_it 0.623 r_mcangle_it 0.406 r_scbond_it 0.394 r_nbtor_refined 0.301 r_mcbond_it 0.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.913 r_dihedral_angle_3_deg 18.123 r_dihedral_angle_4_deg 15.58 r_dihedral_angle_1_deg 5.23 r_angle_refined_deg 1.048 r_scangle_it 0.623 r_mcangle_it 0.406 r_scbond_it 0.394 r_nbtor_refined 0.301 r_mcbond_it 0.224 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.156 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.08 r_symmetry_hbond_refined 0.078 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 39054 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 414
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling