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Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A complexed with 3-aminooxypropionic acid
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 0.02M Sodium/potassium phosphate, 0.1M Bis-Tris propane pH 6.5, 20% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.102 α = 90 b = 51.335 β = 110.03 c = 205.289 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 2022-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 0.75268
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 2.1 47.55 98 0.115 0.132 0.063 0.994 7.9 4.2 79705
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 2.1 2.14 96.2 0.698 0.8 0.387 0.658 4.1
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 2.1 47.55 75709 3973 97.83 0.25809 0.2559 0.2593 0.29834 0.2971 RANDOM 37.564
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] -0.6 0.69 0.64 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.545 r_dihedral_angle_4_deg 20.104 r_dihedral_angle_3_deg 17.154 r_dihedral_angle_1_deg 7.52 r_long_range_B_refined 5.06 r_long_range_B_other 5.057 r_scangle_other 3.216 r_mcangle_it 3.105 r_mcangle_other 3.105 r_scbond_other 2.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.545 r_dihedral_angle_4_deg 20.104 r_dihedral_angle_3_deg 17.154 r_dihedral_angle_1_deg 7.52 r_long_range_B_refined 5.06 r_long_range_B_other 5.057 r_scangle_other 3.216 r_mcangle_it 3.105 r_mcangle_other 3.105 r_scbond_other 2.067 r_scbond_it 2.066 r_angle_refined_deg 2.039 r_mcbond_it 1.984 r_mcbond_other 1.984 r_angle_other_deg 1.365 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 10513 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction