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Crystal structure of D-aminoacid transaminase from Haliscomenobacter hydrossis in its intermediate form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CM0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 MES 0.1 M pH 6.5; MgSO4; 1.8 M NaCl.
Crystal Properties Matthews coefficient Solvent content 2.5 50.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.636 α = 90 b = 72.374 β = 100.05 c = 51.822 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 DECTRIS EIGER X 16M 2021-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.97 ESRF MASSIF-3
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 1.95 51.03 97.5 0.048 0.059 0.033 0.998 10.9 2.9 22696
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 1.95 2 95.6 0.394 0.476 0.265 0.885 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5CM0 1.95 39.87 21576 1105 97.35 0.19323 0.19115 0.1912 0.23153 0.2317 RANDOM 32.572
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] 0.53 -2.25 -0.24 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.849 r_dihedral_angle_4_deg 21.435 r_dihedral_angle_3_deg 15.055 r_long_range_B_refined 7.51 r_dihedral_angle_1_deg 6.788 r_mcangle_it 4.172 r_scbond_it 3.982 r_mcbond_it 3.064 r_angle_refined_deg 1.533 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.849 r_dihedral_angle_4_deg 21.435 r_dihedral_angle_3_deg 15.055 r_long_range_B_refined 7.51 r_dihedral_angle_1_deg 6.788 r_mcangle_it 4.172 r_scbond_it 3.982 r_mcbond_it 3.064 r_angle_refined_deg 1.533 r_chiral_restr 0.114 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2163 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction DIALS data reduction