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Crystal structure of meso-diaminopimelate dehydrogenase from Bacillus thermozeamaize mutant M9 complexed with NADP+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ZMX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.75 291 20 mM sodium formate; 20 mM ammonium acetate; 20 mM sodium citrate tribasic dihydrate; 20 mM potassium sodium tartrate tetrahydrate; 20 mM sodium oxamate; 100 mM MES/imidazole, pH 6.75; 20% (v/v) ethylene glycol and 10% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.98 58.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.07 α = 90 b = 156.07 β = 90 c = 112.31 γ = 90
Symmetry Space Group P 43 21 2
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 EIGER2 S 9M 2024-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.987 SSRL BL12-1
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 2.65 50.05 100 0.999 17 26.6 40873 55.66
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 2.65 2.76 0.848
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8ZMX 2.65 50.05 1.35 40792 1976 99.93 0.2028 0.2011 0.2375 0.2054 66.67
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.8985 f_angle_d 0.7182 f_chiral_restr 0.0502 f_plane_restr 0.0042 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7051 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 206
Software Software Software Name Purpose PHENIX refinement PHENIX refinement autoPROC data reduction Aimless data scaling PHASER phasing