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Crystal structure of a putative short-chain dehydrogenase/reductase from Mycobacterium abscessus bound to NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OEC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 MyabA.01326.f.A1 PW30378 at 27.3 mg/mL against JCSG+ screen condition D10, 0.2 M Ca(OAc)2, 0.1 M Na cacodylate pH 6.5, 40% PEG 300, direct cryo, crsytal tracking ID 219629d10, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.36 47.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.36 α = 81.77 b = 84.97 β = 76.78 c = 100.89 γ = 74.23
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+ 2011-03-24 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 2.1 50 94.9 0.104 11.14 3.9 125503 119101 -3 18.864
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 2.1 2.15 89.3 0.249 5.59 3.6 9192
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 3oec 2.1 50 119100 5974 94.95 0.1917 0.1893 0.194 0.237 0.1978 RANDOM 12.2523
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] -0.34 -0.18 -0.39 0.4 0.38 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.07 r_dihedral_angle_4_deg 15.913 r_dihedral_angle_3_deg 13.639 r_dihedral_angle_1_deg 6.163 r_scangle_it 3.008 r_scbond_it 1.902 r_angle_refined_deg 1.484 r_mcangle_it 1.1 r_mcbond_it 0.628 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.07 r_dihedral_angle_4_deg 15.913 r_dihedral_angle_3_deg 13.639 r_dihedral_angle_1_deg 6.163 r_scangle_it 3.008 r_scbond_it 1.902 r_angle_refined_deg 1.484 r_mcangle_it 1.1 r_mcbond_it 0.628 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15649 Nucleic Acid Atoms Solvent Atoms 1254 Heterogen Atoms 360
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction