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Meso-Diaminopimelate dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8I78
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 0.1M Sodium acetate trihydrate,2M ammonium sulfate, pH 4.5
Crystal Properties Matthews coefficient Solvent content 4.17 70.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 213.3 α = 90 b = 213.3 β = 90 c = 245.84 γ = 120
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 2022-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.541
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.02 47.29 97 0.98 8 5.7 40836
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.02 3.14 96.4 0.701 4.4
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 3.02 47 38848 1981 96.63 0.20905 0.20735 0.24335 0.2035 RANDOM 35.564
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] -1.39 -0.69 -1.39 4.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.723 r_dihedral_angle_4_deg 19.899 r_dihedral_angle_3_deg 15.394 r_dihedral_angle_1_deg 7.213 r_long_range_B_refined 6.467 r_long_range_B_other 6.466 r_scangle_other 4.388 r_mcangle_it 3.551 r_mcangle_other 3.551 r_scbond_it 2.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.723 r_dihedral_angle_4_deg 19.899 r_dihedral_angle_3_deg 15.394 r_dihedral_angle_1_deg 7.213 r_long_range_B_refined 6.467 r_long_range_B_other 6.466 r_scangle_other 4.388 r_mcangle_it 3.551 r_mcangle_other 3.551 r_scbond_it 2.71 r_scbond_other 2.67 r_mcbond_it 2.215 r_mcbond_other 2.215 r_angle_refined_deg 1.44 r_angle_other_deg 1.189 r_chiral_restr 0.055 r_bond_refined_d 0.006 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 8980 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 179
Software Software Software Name Purpose PHENIX refinement