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Crystal structure of a short-chain type dehydrogenase/reductase from Mycobacterium marinum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CTM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 MymaA.01365.b.A1 PS00949 at 55 mg/mL against JCSF+ screen condition D6, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% PEG 8000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220110d6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.45 49.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.52 α = 90 b = 127.91 β = 90 c = 105.65 γ = 90
Symmetry Space Group C 2 2 21
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+ VariMax 2011-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.95 50 99.4 0.06 19.5 5.4 42084 41849 -3 27.831
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 1.95 2 99.4 0.43 3.14 3.2 3084
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 3ctm 1.95 39.24 41760 2105 99.24 0.1655 0.1637 0.1697 0.197 0.2012 RANDOM 21.951
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] -0.53 1.38 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.177 r_dihedral_angle_3_deg 11.423 r_dihedral_angle_4_deg 10.836 r_dihedral_angle_1_deg 5.449 r_scangle_it 3.323 r_scbond_it 2.001 r_angle_refined_deg 1.303 r_mcangle_it 1.179 r_mcbond_it 0.675 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.177 r_dihedral_angle_3_deg 11.423 r_dihedral_angle_4_deg 10.836 r_dihedral_angle_1_deg 5.449 r_scangle_it 3.323 r_scbond_it 2.001 r_angle_refined_deg 1.303 r_mcangle_it 1.179 r_mcbond_it 0.675 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3645 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 6
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction