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proline racemase in complex with one molecule of pyrrole-2-carboxylic acid (hemi form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W61 PDB ENTRY 1W61
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 15% PEG 4000,100MM NH4ACETATE 50MM NA3CITRATE.H2O,PH5.6, pH 5.60
Crystal Properties Matthews coefficient Solvent content 2.6 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.018 α = 90 b = 89.382 β = 125.98 c = 84.456 γ = 90
Symmetry Space Group C 1 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 110 CCD ADSC CCD SAGITALLY FOCUSING GE(220) AND A MULTILAYER M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 60 97.6 0.08 10 2.4 27664 2 54.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 97.4 0.22 4 2.4
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 (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 1W61 2.5 30 24875 2778 97.3 0.177 0.17 0.1791 0.236 0.2412 RANDOM 37.8
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] -0.13 -0.66 -0.38 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.371 r_dihedral_angle_3_deg 17.165 r_dihedral_angle_4_deg 15.459 r_dihedral_angle_1_deg 7.114 r_scangle_it 2.967 r_scbond_it 1.875 r_angle_refined_deg 1.766 r_mcangle_it 1.201 r_mcbond_it 1.011 r_angle_other_deg 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.371 r_dihedral_angle_3_deg 17.165 r_dihedral_angle_4_deg 15.459 r_dihedral_angle_1_deg 7.114 r_scangle_it 2.967 r_scbond_it 1.875 r_angle_refined_deg 1.766 r_mcangle_it 1.201 r_mcbond_it 1.011 r_angle_other_deg 0.88 r_symmetry_hbond_refined 0.287 r_symmetry_vdw_refined 0.219 r_symmetry_vdw_other 0.217 r_nbd_refined 0.208 r_nbd_other 0.185 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.099 r_nbtor_other 0.089 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5395 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing