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Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis in the holo form obtained at pH 7.0
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 7 288 45% v/v Tacsimate pH 7.0, 0.1 M BIS-TRIS propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.45 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.043 α = 90 b = 71.902 β = 100.14 c = 52.015 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 2023-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 21.96 99.7 0.075 0.081 0.032 0.998 23.7 6.6 21090
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 97.6 0.391 0.425 0.164 0.926 6.6
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 21.96 20100 988 99.71 0.14716 0.14505 0.1581 0.19038 0.2008 RANDOM 23.137
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] 0.33 -0.82 -0.17 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.848 r_dihedral_angle_2_deg 10.611 r_long_range_B_other 8.1 r_long_range_B_refined 8.096 r_dihedral_angle_1_deg 6.993 r_scangle_other 6.583 r_scbond_other 4.412 r_scbond_it 4.407 r_mcangle_it 3.632 r_mcangle_other 3.632
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.848 r_dihedral_angle_2_deg 10.611 r_long_range_B_other 8.1 r_long_range_B_refined 8.096 r_dihedral_angle_1_deg 6.993 r_scangle_other 6.583 r_scbond_other 4.412 r_scbond_it 4.407 r_mcangle_it 3.632 r_mcangle_other 3.632 r_mcbond_it 2.767 r_mcbond_other 2.762 r_angle_refined_deg 2.285 r_angle_other_deg 0.759 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2273 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling CrysalisPro data reduction MOLREP phasing PDB_EXTRACT data extraction