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Crystal structure of the alanine racemase Bsu17640 from Bacillus subtilis in the presence of HEPES
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IRP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 290 15% PEG 4000, 0.2 MgCl2, 0.1 M Hepes
Crystal Properties Matthews coefficient Solvent content 2.59 52.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.655 α = 90 b = 73.655 β = 90 c = 331.612 γ = 90
Symmetry Space Group P 43 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 PILATUS 6M 2016-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979340 ALBA XALOC
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 2.05 49.29 99 0.1 0.05 0.99 10.1 16.5 58818
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.11
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 5IRP 2.05 49.29 55776 2927 99.9 0.18786 0.18529 0.1973 0.2373 0.2453 RANDOM 44.455
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] 0.67 0.67 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.048 r_dihedral_angle_4_deg 22.204 r_dihedral_angle_3_deg 15.832 r_dihedral_angle_1_deg 7.372 r_long_range_B_refined 5.722 r_long_range_B_other 5.696 r_scangle_other 4.214 r_mcangle_it 2.891 r_mcangle_other 2.891 r_scbond_it 2.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.048 r_dihedral_angle_4_deg 22.204 r_dihedral_angle_3_deg 15.832 r_dihedral_angle_1_deg 7.372 r_long_range_B_refined 5.722 r_long_range_B_other 5.696 r_scangle_other 4.214 r_mcangle_it 2.891 r_mcangle_other 2.891 r_scbond_it 2.833 r_scbond_other 2.833 r_angle_refined_deg 2.376 r_mcbond_it 2.069 r_mcbond_other 2.062 r_angle_other_deg 1.19 r_chiral_restr 0.139 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d 0.002 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 6050 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Coot model building