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Structure of Mycobacterium tuberculosis NadD in complex with NADP, P21212
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4S1O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.87 298 0.1M HEPES pH 7.5, 1.26M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.45 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.04 α = 90 b = 141.43 β = 90 c = 63.17 γ = 90
Symmetry Space Group P 21 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 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 0.97903 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.65 70.71 98.9 0.064 0.071 16.45 5.5 53894 53277 -3 28.953
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.74 92.4 0.823 0.999 2.19 4.7
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 4S1O 1.65 70.71 53277 2656 98.85 0.1911 0.1898 0.1997 0.2163 0.2221 RANDOM 25.641
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] -0.1 -0.64 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.677 r_dihedral_angle_4_deg 16.215 r_dihedral_angle_3_deg 10.562 r_dihedral_angle_1_deg 5.704 r_mcangle_it 2.433 r_mcbond_it 1.533 r_mcbond_other 1.528 r_angle_refined_deg 1.371 r_angle_other_deg 0.939 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.677 r_dihedral_angle_4_deg 16.215 r_dihedral_angle_3_deg 10.562 r_dihedral_angle_1_deg 5.704 r_mcangle_it 2.433 r_mcbond_it 1.533 r_mcbond_other 1.528 r_angle_refined_deg 1.371 r_angle_other_deg 0.939 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3069 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 138
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction