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Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant R88L
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 Sodium nitrate, 0.1 M Bis-Tris propane pH 6.5, 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.791 α = 90 b = 88.553 β = 90 c = 100.663 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 PIXEL RIGAKU HyPix-6000HE 2021-11-17 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 88.55 99.6 0.093 0.102 0.041 0.998 14.3 6 50878
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 95.8 1.108 1.345 0.746 0.389 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 66.49 48313 2498 99.41 0.19069 0.18922 0.1995 0.219 0.226 RANDOM 24.654
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] -0.65 0.38 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.524 r_dihedral_angle_4_deg 19.048 r_dihedral_angle_3_deg 14.128 r_dihedral_angle_1_deg 7.141 r_long_range_B_refined 5.83 r_long_range_B_other 5.815 r_scangle_other 4.852 r_scbond_it 3.272 r_scbond_other 3.271 r_mcangle_it 3.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.524 r_dihedral_angle_4_deg 19.048 r_dihedral_angle_3_deg 14.128 r_dihedral_angle_1_deg 7.141 r_long_range_B_refined 5.83 r_long_range_B_other 5.815 r_scangle_other 4.852 r_scbond_it 3.272 r_scbond_other 3.271 r_mcangle_it 3.257 r_mcangle_other 3.257 r_mcbond_it 2.395 r_mcbond_other 2.395 r_angle_refined_deg 1.719 r_angle_other_deg 1.522 r_chiral_restr 0.088 r_bond_refined_d 0.012 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 4209 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction