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Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis complexed with 3-aminooxypropionic acid
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 0.2M MgCl2, 0.1M Bis-tris pH 5.5, 25%
PEG 3350, 6mM PLP, 12mM 3-aminooxypropionic acid
Crystal Properties Matthews coefficient Solvent content 2.46 50.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.772 α = 90 b = 71.232 β = 101.26 c = 52.549 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 CCD MAR CCD 165 mm 2022-06-03 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 1.7 35.34 94.9 0.083 0.1 0.054 0.991 11.4 3.3 32789
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 1.7 1.73 98.6 0.484 0.578 0.312 0.602 3.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.7 35.34 31120 1667 94.87 0.16793 0.16569 0.2104 0.1923 RANDOM 16.275
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] -0.66 -0.28 0.2 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.389 r_dihedral_angle_4_deg 18.047 r_dihedral_angle_3_deg 14.363 r_dihedral_angle_1_deg 6.985 r_long_range_B_refined 4.968 r_long_range_B_other 4.777 r_scangle_other 3.341 r_scbond_it 2.15 r_scbond_other 2.129 r_mcangle_it 2.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.389 r_dihedral_angle_4_deg 18.047 r_dihedral_angle_3_deg 14.363 r_dihedral_angle_1_deg 6.985 r_long_range_B_refined 4.968 r_long_range_B_other 4.777 r_scangle_other 3.341 r_scbond_it 2.15 r_scbond_other 2.129 r_mcangle_it 2.128 r_mcangle_other 2.128 r_angle_refined_deg 1.672 r_mcbond_it 1.44 r_mcbond_other 1.439 r_angle_other_deg 1.428 r_chiral_restr 0.081 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 2226 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction DIALS data reduction MOLREP phasing