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Crystal structure of D-amino acid aminotransferase from Blastococcus saxobsidens complexed with phenylhydrazine and in its apo 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 2.81 56.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.644 α = 90 b = 104.644 β = 90 c = 51.541 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 2023-03-31 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 22.59 99.6 0.215 0.224 0.062 0.996 10.7 12.9 30251
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 96.6 1.52 1.583 0.437 0.506 12.8
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 1.8 22.59 28796 1429 99.43 0.20568 0.20322 0.2094 0.25406 0.2577 RANDOM 17.585
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] 0.15 0.07 0.15 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.283 r_dihedral_angle_4_deg 18.131 r_dihedral_angle_3_deg 15.798 r_dihedral_angle_1_deg 6.929 r_long_range_B_refined 4.941 r_long_range_B_other 4.822 r_scangle_other 3.078 r_mcangle_it 2.575 r_mcangle_other 2.575 r_scbond_it 1.962
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.283 r_dihedral_angle_4_deg 18.131 r_dihedral_angle_3_deg 15.798 r_dihedral_angle_1_deg 6.929 r_long_range_B_refined 4.941 r_long_range_B_other 4.822 r_scangle_other 3.078 r_mcangle_it 2.575 r_mcangle_other 2.575 r_scbond_it 1.962 r_scbond_other 1.961 r_angle_refined_deg 1.79 r_mcbond_it 1.644 r_mcbond_other 1.642 r_angle_other_deg 1.444 r_chiral_restr 0.078 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 2007 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement Aimless data scaling CrysalisPro data reduction MOLREP phasing PDB_EXTRACT data extraction