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Crystal structure of Short-chain dehydrogenase/reductase SDR from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2UVD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Internal tracking number 216858D10. JCSG+ screen
condition D10:
0.2 M CaOAc2, 0.1 M MES cacodylate pH 6.5, 40% PEG300, MysmA.01365.d.A1
PW 28823 at 28.7 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.56 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.14 α = 90 b = 78.01 β = 102.22 c = 155.43 γ = 90
Symmetry Space Group C 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 CCD RIGAKU SATURN 944+ 2010-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.541780
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 1.75 41.23 96.1 0.057 20.47 7.53 106123 102002 -3 24.209
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 1.75 1.8 85.2 0.48 3.2 4.57 7786
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 2UVD 1.75 41.23 106123 101895 5101 96.03 0.152 0.152 0.15 0.16 0.183 0.1889 RANDOM 18.491
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] -0.03 -0.08 0.27 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.896 r_dihedral_angle_4_deg 18.681 r_dihedral_angle_3_deg 11.905 r_dihedral_angle_1_deg 5.518 r_scangle_it 4.273 r_scbond_it 2.543 r_angle_refined_deg 1.52 r_mcangle_it 1.483 r_angle_other_deg 0.997 r_mcbond_it 0.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.896 r_dihedral_angle_4_deg 18.681 r_dihedral_angle_3_deg 11.905 r_dihedral_angle_1_deg 5.518 r_scangle_it 4.273 r_scbond_it 2.543 r_angle_refined_deg 1.52 r_mcangle_it 1.483 r_angle_other_deg 0.997 r_mcbond_it 0.882 r_mcbond_other 0.283 r_chiral_restr 0.097 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7293 Nucleic Acid Atoms Solvent Atoms 878 Heterogen Atoms 59
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction