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Structure of a meso-diaminopimelate dehydrogenase in complex with NADP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 trisodium citrate dihydrate, TES, NADP, D-Lys, pH 7.5, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.79 67.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.021 α = 90 b = 123.021 β = 90 c = 193.302 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 2013-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 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 2.07 50 99.9 0.084 14.8 5.6 66282 66282
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 2.07 2.14 100 0.296 5.7 6609
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 2.07 31.12 66282 66282 3365 99.79 0.1752 0.1752 0.1734 0.186 0.2084 0.2112 RANDOM 34.372
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] 0.36 0.36 0.36 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.379 r_dihedral_angle_4_deg 15.584 r_dihedral_angle_3_deg 15.408 r_dihedral_angle_1_deg 6.965 r_mcangle_it 4.08 r_mcbond_it 3.237 r_mcbond_other 3.214 r_angle_refined_deg 2.067 r_angle_other_deg 0.938 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.379 r_dihedral_angle_4_deg 15.584 r_dihedral_angle_3_deg 15.408 r_dihedral_angle_1_deg 6.965 r_mcangle_it 4.08 r_mcbond_it 3.237 r_mcbond_other 3.214 r_angle_refined_deg 2.067 r_angle_other_deg 0.938 r_chiral_restr 0.135 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5084 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 152
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing