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Proline Racemase (ProR) from the Gram-positive bacterium Acetoanaerobium sticklandii from isotropic tetragonal data at 3.15 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, HANGING DROP 7 291 1.26 M Ammonium Sulphate, 100 mM Cacodylate, pH 6.5 at rtp
Crystal Properties Matthews coefficient Solvent content 2.08 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.724 α = 90 b = 109.724 β = 90 c = 104.99 γ = 90
Symmetry Space Group P 43 21 2
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 2018-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 3.15 109.1 100 0.267 0.115 0.994 6.8 11.6 11620
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 3.15 3.37 100 3.32 1.335 0.457 1.2 12.3
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 3.15 77.707 11583 690 99.965 0.27 0.2657 0.2649 0.3301 0.3288 127.154
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] -0.476 -0.476 0.951
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.592 r_dihedral_angle_3_deg 21.688 r_dihedral_angle_4_deg 19.89 r_dihedral_angle_1_deg 11.552 r_lrange_it 5.457 r_lrange_other 5.456 r_angle_refined_deg 1.718 r_mcangle_it 1.179 r_mcangle_other 1.179 r_angle_other_deg 1.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.592 r_dihedral_angle_3_deg 21.688 r_dihedral_angle_4_deg 19.89 r_dihedral_angle_1_deg 11.552 r_lrange_it 5.457 r_lrange_other 5.456 r_angle_refined_deg 1.718 r_mcangle_it 1.179 r_mcangle_other 1.179 r_angle_other_deg 1.088 r_scangle_it 0.974 r_scangle_other 0.974 r_mcbond_it 0.664 r_mcbond_other 0.664 r_scbond_other 0.522 r_scbond_it 0.521 r_nbd_refined 0.25 r_symmetry_nbd_refined 0.247 r_symmetry_nbd_other 0.235 r_xyhbond_nbd_refined 0.23 r_nbd_other 0.21 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.15 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.022 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5172 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data scaling PHASER phasing