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Crystal structure of D-amino acid aminotransferase from Blastococcus saxobsidens in PMP form
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 2.83 56.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.437 α = 90 b = 105.437 β = 90 c = 51.144 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 RIGAKU HyPix-6000HE 2022-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54184
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 1.8 20.55 99.2 0.111 0.114 0.028 0.999 23.2 15.9 30325
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 1.8 1.84 95.9 0.462 0.482 0.133 0.836 12.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 20.55 28882 1431 99.1 0.17795 0.17628 0.21079 0.2188 RANDOM 10.965
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] 2.32 2.32 -4.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.644 r_dihedral_angle_3_deg 15.966 r_dihedral_angle_4_deg 15.68 r_dihedral_angle_1_deg 6.531 r_long_range_B_refined 3.675 r_long_range_B_other 3.546 r_scangle_other 2.031 r_mcangle_it 1.781 r_mcangle_other 1.78 r_angle_refined_deg 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.644 r_dihedral_angle_3_deg 15.966 r_dihedral_angle_4_deg 15.68 r_dihedral_angle_1_deg 6.531 r_long_range_B_refined 3.675 r_long_range_B_other 3.546 r_scangle_other 2.031 r_mcangle_it 1.781 r_mcangle_other 1.78 r_angle_refined_deg 1.75 r_angle_other_deg 1.425 r_scbond_it 1.288 r_scbond_other 1.287 r_mcbond_it 1.086 r_mcbond_other 1.084 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 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 253 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement Aimless data scaling CrysalisPro data reduction MOLREP phasing PDB_EXTRACT data extraction