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Crystal structure of D-amino acid aminotransferase from Blastococcus saxobsidens in holo form with PLP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q1R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 0.1 M Hepes pH 7.5, 4 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.86 57.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.935 α = 90 b = 105.935 β = 90 c = 51.324 γ = 120
Symmetry Space Group P 31 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 100 PIXEL DECTRIS PILATUS 6M 2021-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.96770 ESRF ID23-1
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 1.7 52.97 97.4 0.083 0.098 0.051 0.994 10.1 3.5 35723
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 1.7 1.73 91.5 0.481 0.586 0.33 0.792 2.8
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 1.7 52.97 34008 1700 97.25 0.172 0.17094 0.1816 0.19246 0.1981 RANDOM 22.373
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] 0.54 0.27 0.54 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.562 r_dihedral_angle_4_deg 14.95 r_dihedral_angle_3_deg 13.278 r_dihedral_angle_1_deg 6.042 r_long_range_B_refined 5.061 r_long_range_B_other 4.96 r_scangle_other 4.095 r_scbond_other 2.802 r_scbond_it 2.798 r_mcangle_it 2.597
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.562 r_dihedral_angle_4_deg 14.95 r_dihedral_angle_3_deg 13.278 r_dihedral_angle_1_deg 6.042 r_long_range_B_refined 5.061 r_long_range_B_other 4.96 r_scangle_other 4.095 r_scbond_other 2.802 r_scbond_it 2.798 r_mcangle_it 2.597 r_mcangle_other 2.597 r_mcbond_it 1.821 r_mcbond_other 1.818 r_angle_refined_deg 1.686 r_angle_other_deg 1.494 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 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 2020 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing PDB_EXTRACT data extraction