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Crystal structure of meso-diaminopimelate dehydrogenase from Prevotella timonensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M HEPES, pH 7.5, 0.1 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.51 51.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.73 α = 90 b = 189.6 β = 90 c = 101.82 γ = 90
Symmetry Space Group C 2 2 21
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 Bruker PHOTON II 2021-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.07 47.53 99.8 0.173 7.8 4.7 18754
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.07 3.28 0.66
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 3.07 47.53 17866 870 99.63 0.2007 0.19786 0.26051 0.2153 RANDOM 52.028
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] -2.66 0.04 2.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.821 r_dihedral_angle_4_deg 20.002 r_dihedral_angle_3_deg 18.302 r_long_range_B_refined 9.711 r_long_range_B_other 9.71 r_dihedral_angle_1_deg 7.827 r_scangle_other 6.677 r_mcangle_it 6.134 r_mcangle_other 6.133 r_scbond_it 4.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.821 r_dihedral_angle_4_deg 20.002 r_dihedral_angle_3_deg 18.302 r_long_range_B_refined 9.711 r_long_range_B_other 9.71 r_dihedral_angle_1_deg 7.827 r_scangle_other 6.677 r_mcangle_it 6.134 r_mcangle_other 6.133 r_scbond_it 4.157 r_scbond_other 4.145 r_mcbond_it 3.885 r_mcbond_other 3.884 r_angle_refined_deg 1.485 r_angle_other_deg 1.157 r_chiral_restr 0.053 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 6804 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 220
Software Software Software Name Purpose Aimless data scaling HKL-2000 data reduction