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Crystal structure of probable short-chain dehydrogenase-reductase from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IY8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 Emerald Wizard Full screen condition F6, 20% PEG 3000, 0.1 M Tris, 0.2 M CaCl2, 11.8 mg/mL protein, crystal ID 202293f6, 25% glycerol as cryo-protectant, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.21 44.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.69 α = 90 b = 51.38 β = 94.5 c = 118.84 γ = 90
Symmetry Space Group P 1 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 2009-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97933 APS 23-ID-D
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 2.45 20 98.8 0.135 7.97 36246 -3 32.734
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 2.45 2.51 99.5 0.561 2.2 2654
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 1IY8 2.45 19.9 36246 1808 98.78 0.195 0.192 0.198 0.247 0.1971 RANDOM 25.165
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] 2.84 2.01 -1.98 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.777 r_dihedral_angle_3_deg 15.139 r_dihedral_angle_4_deg 13.464 r_dihedral_angle_1_deg 5.804 r_scangle_it 2.213 r_scbond_it 1.304 r_angle_refined_deg 1.176 r_mcangle_it 0.885 r_angle_other_deg 0.872 r_mcbond_it 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.777 r_dihedral_angle_3_deg 15.139 r_dihedral_angle_4_deg 13.464 r_dihedral_angle_1_deg 5.804 r_scangle_it 2.213 r_scbond_it 1.304 r_angle_refined_deg 1.176 r_mcangle_it 0.885 r_angle_other_deg 0.872 r_mcbond_it 0.47 r_mcbond_other 0.072 r_chiral_restr 0.062 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6983 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction