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Amino acid racemase in complex with PLP-L-Ile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WYA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 MPD, Na acetate buffer
Crystal Properties Matthews coefficient Solvent content 2.65 53.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.644 α = 90 b = 132.375 β = 90 c = 136.525 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 PILATUS3 S 2M 2020-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.87 50 92.5 0.99 7.6 4.5 24849
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.87 2.94 95.5 0.511 0.579 0.267 0.829 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.87 47.56 23664 1151 91.88 0.1896 0.18636 0.1903 0.25806 0.2505 RANDOM 61.455
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] 2.07 0.51 -2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.484 r_dihedral_angle_4_deg 20.062 r_dihedral_angle_3_deg 19.082 r_long_range_B_refined 9.203 r_long_range_B_other 9.203 r_dihedral_angle_1_deg 7.165 r_scangle_other 6.944 r_mcangle_other 6.2 r_mcangle_it 6.199 r_scbond_it 4.388
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.484 r_dihedral_angle_4_deg 20.062 r_dihedral_angle_3_deg 19.082 r_long_range_B_refined 9.203 r_long_range_B_other 9.203 r_dihedral_angle_1_deg 7.165 r_scangle_other 6.944 r_mcangle_other 6.2 r_mcangle_it 6.199 r_scbond_it 4.388 r_scbond_other 4.387 r_mcbond_it 4.206 r_mcbond_other 4.2 r_angle_refined_deg 1.414 r_angle_other_deg 1.292 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7280 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing PDB_EXTRACT data extraction