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Crystal structure of carveol dehydrogenase from Mycobacterium thermoresistibile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IY8 PDB ENTRY 1iy8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 80MM NA-CACOCYLATE PH 6.5, 14.4% PEG 8000, 20% GLYCEROL, protein AT 29.5MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.01 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.86 α = 90 b = 120.57 β = 94.05 c = 134.56 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+ RIGAKU VARIMAX HF 2010-07-12 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 98.9 0.089 10.23 3.6 78522 77636 -3 20.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 96.8 0.316 0.316 2.9 2.2 5832
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 1iy8 1.95 45.74 77535 3898 98.8 0.179 0.176 0.1802 0.233 0.2357 RANDOM 11.8
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] -0.69 -0.14 -0.05 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.059 r_dihedral_angle_4_deg 15.335 r_dihedral_angle_3_deg 13.361 r_dihedral_angle_1_deg 6.672 r_scangle_it 3.756 r_scbond_it 2.332 r_angle_refined_deg 1.536 r_mcangle_it 1.349 r_angle_other_deg 0.969 r_mcbond_it 0.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.059 r_dihedral_angle_4_deg 15.335 r_dihedral_angle_3_deg 13.361 r_dihedral_angle_1_deg 6.672 r_scangle_it 3.756 r_scbond_it 2.332 r_angle_refined_deg 1.536 r_mcangle_it 1.349 r_angle_other_deg 0.969 r_mcbond_it 0.802 r_mcbond_other 0.245 r_chiral_restr 0.093 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8145 Nucleic Acid Atoms Solvent Atoms 821 Heterogen Atoms 4
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling