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Ala/Ser-specific racemase in complex with PLP-D-Ala
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 ammonium sulfate, sodium acetate buffer
Crystal Properties Matthews coefficient Solvent content 1.92 35.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.793 α = 90 b = 100.793 β = 90 c = 159.261 γ = 90
Symmetry Space Group I 4 2 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 PILATUS3 S 6M 2024-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.16 47.01 100 0.16 0.164 0.033 0.999 19.7 24.1 22415
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 2.16 2.23 100 1.659 1.723 0.455 0.787 13.9
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 2.16 47.01 21339 1073 99.97 0.1844 0.18169 0.1921 0.23813 0.2373 RANDOM 41.265
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] 2.31 2.31 -4.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.301 r_dihedral_angle_2_deg 15.378 r_long_range_B_refined 8.048 r_long_range_B_other 8.048 r_dihedral_angle_1_deg 6.641 r_scangle_other 6.532 r_scbond_it 4.144 r_scbond_other 4.143 r_mcangle_other 4.111 r_mcangle_it 4.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.301 r_dihedral_angle_2_deg 15.378 r_long_range_B_refined 8.048 r_long_range_B_other 8.048 r_dihedral_angle_1_deg 6.641 r_scangle_other 6.532 r_scbond_it 4.144 r_scbond_other 4.143 r_mcangle_other 4.111 r_mcangle_it 4.11 r_mcbond_it 2.903 r_mcbond_other 2.902 r_angle_refined_deg 1.428 r_angle_other_deg 0.495 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3565 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction