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Structure of 4-Hydroxytetrahydrodipicolinate Reductase from Mycobacterium tuberculosis with NADPH and 2,6 Pyridine Dicarboxylic Acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C3V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M Sodium Chloride, 0.1 M Bis-Tris pH 6.5, 1.5 M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 3.19 61.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.157 α = 90 b = 67.157 β = 90 c = 251.325 γ = 120
Symmetry Space Group P 62 2 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 CCD ADSC QUANTUM 315r 2014-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1 APS 19-ID
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 1.5 30 95.1 0.054 11.4 7.6 52243
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 97.8 0.537 0.792 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1C3V 1.5 30 49673 2565 95.14 0.1486 0.1476 0.1515 0.1687 0.171 RANDOM 29.958
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] -0.26 -0.13 -0.26 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.648 r_dihedral_angle_4_deg 18.114 r_dihedral_angle_3_deg 11.401 r_dihedral_angle_1_deg 5.483 r_scbond_it 2.354 r_angle_refined_deg 2.036 r_mcangle_it 1.718 r_mcbond_it 1.12 r_chiral_restr 0.147 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.648 r_dihedral_angle_4_deg 18.114 r_dihedral_angle_3_deg 11.401 r_dihedral_angle_1_deg 5.483 r_scbond_it 2.354 r_angle_refined_deg 2.036 r_mcangle_it 1.718 r_mcbond_it 1.12 r_chiral_restr 0.147 r_bond_refined_d 0.019 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1807 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 127
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-2000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 phasing