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Crystal structure of a putative carveol dehydrogenase from Mycobacterium paratuberculosis bound to nicotinamide adenine dinucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OEC PDB ENTRY 3oec
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 protein at 23.8 mg/mL in 20 mM Hepes pH 7, 300 mM NaCl, 5% glycerol, DTT, 0.2 M MgCl2, 0.1 M Bis Tris, 25% PEG 3350 with 25% ethylene glycol as cryo-protectant, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.11 41.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.03 α = 90 b = 57.92 β = 91.35 c = 131.74 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 ADSC QUANTUM 315r 2010-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97946 ALS 5.0.3
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 1.85 50 97.9 0.093 14.15 4.6 84005 82274 -3 21.352
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 1.85 1.9 97 0.471 3.6 4.7 6159
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 PDB ENTRY 3oec 1.85 50 82151 4114 97.8 0.1471 0.1446 0.1495 0.1949 0.1986 RANDOM 15.0129
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] 0.97 0.11 -0.56 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.862 r_dihedral_angle_4_deg 16.07 r_dihedral_angle_3_deg 11.349 r_dihedral_angle_1_deg 5.787 r_scangle_it 3.14 r_scbond_it 2.039 r_angle_refined_deg 1.484 r_mcangle_it 1.189 r_mcbond_it 0.719 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.862 r_dihedral_angle_4_deg 16.07 r_dihedral_angle_3_deg 11.349 r_dihedral_angle_1_deg 5.787 r_scangle_it 3.14 r_scbond_it 2.039 r_angle_refined_deg 1.484 r_mcangle_it 1.189 r_mcbond_it 0.719 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7942 Nucleic Acid Atoms Solvent Atoms 969 Heterogen Atoms 176
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction