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Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis point mutant R90I (holo form)
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 2.47 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.392 α = 90 b = 72.627 β = 100.8 c = 52.244 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 2022-12-19 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 21.77 99.4 0.163 0.177 0.069 0.989 7 6.4 21132
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 95 0.388 0.431 0.184 0.92 5.2
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 21.77 19891 1097 98.71 0.19649 0.19419 0.2016 0.23634 0.2401 RANDOM 14.528
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] -1.36 -0.92 -0.76 2.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.312 r_dihedral_angle_4_deg 21.122 r_dihedral_angle_3_deg 14.401 r_dihedral_angle_1_deg 7.329 r_long_range_B_refined 4.361 r_long_range_B_other 4.281 r_scangle_other 3.005 r_scbond_other 1.91 r_scbond_it 1.908 r_mcangle_it 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.312 r_dihedral_angle_4_deg 21.122 r_dihedral_angle_3_deg 14.401 r_dihedral_angle_1_deg 7.329 r_long_range_B_refined 4.361 r_long_range_B_other 4.281 r_scangle_other 3.005 r_scbond_other 1.91 r_scbond_it 1.908 r_mcangle_it 1.88 r_mcangle_other 1.88 r_angle_refined_deg 1.819 r_angle_other_deg 1.411 r_mcbond_it 1.245 r_mcbond_other 1.241 r_chiral_restr 0.082 r_bond_refined_d 0.012 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 2255 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling CrysalisPro data reduction REFMAC phasing PDB_EXTRACT data extraction