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Structure of a meso-diaminopimelate dehydrogenase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 ammonium sulfate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.73 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.747 α = 90 b = 121.747 β = 90 c = 194.124 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 CCD ADSC QUANTUM 270 2013-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1 Photon Factory AR-NE3A
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 2.4 50 99.9 0.072 17.4 5.7 41892 41892
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 2.4 2.44 100 0.308 5.6 2101
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.4 30.82 41892 41892 2117 99.78 0.1752 0.1752 0.173 0.1817 0.2151 0.2173 RANDOM 46.982
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] 1.01 1.01 1.01 -3.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.767 r_dihedral_angle_4_deg 21.577 r_dihedral_angle_3_deg 17.57 r_dihedral_angle_1_deg 6.917 r_mcangle_it 5.364 r_mcbond_it 3.986 r_mcbond_other 3.986 r_angle_refined_deg 1.975 r_angle_other_deg 0.933 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.767 r_dihedral_angle_4_deg 21.577 r_dihedral_angle_3_deg 17.57 r_dihedral_angle_1_deg 6.917 r_mcangle_it 5.364 r_mcbond_it 3.986 r_mcbond_other 3.986 r_angle_refined_deg 1.975 r_angle_other_deg 0.933 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5096 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection MOLREP phasing