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Structure of Mycobacterium tuberculosis NadD in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.2M magnesium nitrate, 20% PEG3350, pH 7.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.33 47.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.06 α = 90 b = 66.06 β = 90 c = 165.21 γ = 120
Symmetry Space Group P 31 2 1
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 MARMOSAIC 300 mm CCD 2014-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97949 APS 22-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 1.84 47.03 99.9 0.09 13.57 7.2 37156 37134 -3 32.415
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 1.84 1.89 100 1.016 2.29
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3E27 1.84 47.03 37156 35301 1835 99.88 0.1961 0.1961 0.1941 0.2026 0.2341 0.237 RANDOM 30.679
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] 0.51 0.25 0.51 -1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.322 r_dihedral_angle_4_deg 16.064 r_dihedral_angle_3_deg 11.855 r_dihedral_angle_1_deg 5.904 r_mcangle_it 3.261 r_mcbond_it 2.111 r_mcbond_other 2.107 r_angle_refined_deg 1.611 r_angle_other_deg 0.956 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.322 r_dihedral_angle_4_deg 16.064 r_dihedral_angle_3_deg 11.855 r_dihedral_angle_1_deg 5.904 r_mcangle_it 3.261 r_mcbond_it 2.111 r_mcbond_other 2.107 r_angle_refined_deg 1.611 r_angle_other_deg 0.956 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2709 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 98
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection XDS data reduction