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Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (holo form).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 0.1M Sodium acetate pH 4.8; 18% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.34 47.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.884 α = 90 b = 71.752 β = 100.96 c = 52.992 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 4M 2021-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 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 1.75 52.03 98.1 0.13 0.157 0.087 0.986 3.8 3.1 31622
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 1.75 1.78 98.6 1.492 1.8 0.992 0.447 3.1
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 5E25 2 52.03 20186 985 97.62 0.1831 0.1803 0.1882 0.2437 0.2486 RANDOM 26.227
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] 0.57 -3.02 -1.53 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.193 r_dihedral_angle_4_deg 18.737 r_dihedral_angle_3_deg 14.513 r_dihedral_angle_1_deg 7.92 r_angle_refined_deg 1.949 r_angle_other_deg 1.396 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.193 r_dihedral_angle_4_deg 18.737 r_dihedral_angle_3_deg 14.513 r_dihedral_angle_1_deg 7.92 r_angle_refined_deg 1.949 r_angle_other_deg 1.396 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2272 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 31
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction