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Proline Racemase (ProR) from the Gram-positive bacterium Acetoanaerobium sticklandii from isotropic orthorhombic data at 3.59 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PB3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 1.26 M Ammonium Sulphate, 100 mM Cacodylate, pH 6.5 at rtp
Crystal Properties Matthews coefficient Solvent content 2.85 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.454 α = 90 b = 107.478 β = 90 c = 109.052 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2018-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 3.59 107.48 100 0.196 0.085 0.991 6.4 6.3 14925
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.59 3.93 100 1.015 0.441 0.498 2.1 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7pb3 3.59 76.549 14881 747 99.98 0.265 0.2597 0.2603 0.3599 0.3605 141.755
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] 0.996 0.124 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.233 r_dihedral_angle_3_deg 21.539 r_dihedral_angle_4_deg 15.178 r_lrange_it 11.281 r_lrange_other 11.281 r_dihedral_angle_1_deg 9.777 r_mcangle_it 7.144 r_mcangle_other 7.144 r_scangle_it 6.529 r_scangle_other 6.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.233 r_dihedral_angle_3_deg 21.539 r_dihedral_angle_4_deg 15.178 r_lrange_it 11.281 r_lrange_other 11.281 r_dihedral_angle_1_deg 9.777 r_mcangle_it 7.144 r_mcangle_other 7.144 r_scangle_it 6.529 r_scangle_other 6.529 r_mcbond_it 4.179 r_mcbond_other 4.179 r_scbond_it 3.718 r_scbond_other 3.718 r_angle_other_deg 2.378 r_angle_refined_deg 1.655 r_nbd_other 0.272 r_nbd_refined 0.243 r_symmetry_xyhbond_nbd_refined 0.24 r_symmetry_nbd_other 0.238 r_symmetry_nbd_refined 0.203 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_other 0.16 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.063 r_bond_other_d 0.035 r_xyhbond_nbd_other 0.034 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10344 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data scaling PHASER phasing