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Crystal structure of a putative carveol dehydrogenase from Mycobacterium avium bound to NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TSC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 MyavA.01326.g.A1 PS01550 at 20 mg/mL with 2.5 mM NAD against MCSG1 condition C12, 0.1 M BisTrisHCL pH 6.5, 25% PEG 3350 supplemented with 15% EG as cryo-protectant, crystal tracking ID 257485c12, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.36 47.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.53 α = 90 b = 106.37 β = 90 c = 135.87 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 2014-09-02 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 98.3 0.052 21.84 5.8 43895 43134 -3 32.389
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 92 0.382 2.75
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 3TSC 1.95 50 40966 2168 98.26 0.2082 0.2065 0.2188 0.2411 0.2564 RANDOM 40.776
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] 1.71 -1.75 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.047 r_dihedral_angle_4_deg 20.678 r_dihedral_angle_3_deg 13.531 r_dihedral_angle_1_deg 6.175 r_angle_refined_deg 1.441 r_mcangle_it 1.322 r_angle_other_deg 0.93 r_mcbond_it 0.777 r_mcbond_other 0.772 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.047 r_dihedral_angle_4_deg 20.678 r_dihedral_angle_3_deg 13.531 r_dihedral_angle_1_deg 6.175 r_angle_refined_deg 1.441 r_mcangle_it 1.322 r_angle_other_deg 0.93 r_mcbond_it 0.777 r_mcbond_other 0.772 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4019 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 88
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction