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Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis point mutant R90I complexed with phenylhydrazine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7P7X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 45% (v/v) Tacsimate, 50 mM BISTRIS buffer, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.48 50.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.749 α = 90 b = 72.75 β = 100.77 c = 52.341 γ = 90
Symmetry Space Group C 1 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 2023-03-02 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 2 20.82 99.7 0.06 0.066 0.026 0.999 23 6.6 21415
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 2.05 96.8 0.281 0.304 0.117 0.962 6.7
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 20.82 20275 1117 99.79 0.15801 0.15577 0.1662 0.19626 0.205 RANDOM 20.061
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] -0.49 -0.91 0.11 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.21 r_dihedral_angle_4_deg 20.172 r_dihedral_angle_3_deg 14.22 r_dihedral_angle_1_deg 6.923 r_long_range_B_refined 5.439 r_long_range_B_other 5.386 r_scangle_other 3.933 r_scbond_other 2.565 r_scbond_it 2.564 r_mcangle_it 2.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.21 r_dihedral_angle_4_deg 20.172 r_dihedral_angle_3_deg 14.22 r_dihedral_angle_1_deg 6.923 r_long_range_B_refined 5.439 r_long_range_B_other 5.386 r_scangle_other 3.933 r_scbond_other 2.565 r_scbond_it 2.564 r_mcangle_it 2.511 r_mcangle_other 2.511 r_mcbond_it 1.762 r_mcbond_other 1.757 r_angle_refined_deg 1.684 r_angle_other_deg 1.398 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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 2264 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement Aimless data scaling CrysalisPro data reduction MOLREP phasing PDB_EXTRACT data extraction