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Amino acid racemase in complex with PLP-D-Phe
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 3-methyl-1,5-pentanediol, sodium acetate buffer
Crystal Properties Matthews coefficient Solvent content 2.65 53.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.901 α = 90 b = 133.203 β = 90 c = 135.36 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 2021-03-19 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 2.1 47.5 100 0.99 11.7 6.6 68318
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 0.608
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 2.1 46.51 64838 3398 99.97 0.16975 0.16809 0.181 0.19976 0.2058 RANDOM 40.874
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] -2.35 1.35 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.818 r_dihedral_angle_3_deg 16.34 r_dihedral_angle_4_deg 13.153 r_long_range_B_other 7.829 r_long_range_B_refined 7.828 r_dihedral_angle_1_deg 7.336 r_scangle_other 6.567 r_scbond_it 4.405 r_scbond_other 4.405 r_mcangle_it 4.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.818 r_dihedral_angle_3_deg 16.34 r_dihedral_angle_4_deg 13.153 r_long_range_B_other 7.829 r_long_range_B_refined 7.828 r_dihedral_angle_1_deg 7.336 r_scangle_other 6.567 r_scbond_it 4.405 r_scbond_other 4.405 r_mcangle_it 4.137 r_mcangle_other 4.136 r_mcbond_it 3.111 r_mcbond_other 3.111 r_angle_refined_deg 1.613 r_angle_other_deg 1.347 r_chiral_restr 0.109 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 250 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction