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Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AHR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 288 0.2 M NaNitrate, 0.1 M Bis-tris propane pH 6.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.18 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.429 α = 90 b = 88.013 β = 90 c = 99.772 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2022-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.74503 KURCHATOV SNC K4.4
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 1.9 44.97 99.7 0.11 0.122 0.052 0.997 10.4 5.4 43170
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 1.9 1.94 100 0.69 0.763 0.321 0.731 5.5
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 1.9 33.7 40996 2156 99.51 0.21577 0.21328 0.2196 0.26317 0.2665 RANDOM 26.428
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] -1.52 1.79 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.173 r_dihedral_angle_4_deg 17.082 r_dihedral_angle_3_deg 15.252 r_dihedral_angle_1_deg 7.526 r_long_range_B_refined 5.93 r_long_range_B_other 5.874 r_scangle_other 4.531 r_mcangle_it 3.715 r_mcangle_other 3.715 r_scbond_it 3.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.173 r_dihedral_angle_4_deg 17.082 r_dihedral_angle_3_deg 15.252 r_dihedral_angle_1_deg 7.526 r_long_range_B_refined 5.93 r_long_range_B_other 5.874 r_scangle_other 4.531 r_mcangle_it 3.715 r_mcangle_other 3.715 r_scbond_it 3.135 r_scbond_other 3.135 r_mcbond_it 2.615 r_mcbond_other 2.615 r_angle_refined_deg 1.798 r_angle_other_deg 1.312 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 4207 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction REFMAC phasing PDB_EXTRACT data extraction