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Structure of Iron containing alcohol dehydrogenase from Thermococcus thioreducens in a tetragonal crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C76
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 298 0.4 M NH4H2PO4, pH 4.2
Crystal Properties Matthews coefficient Solvent content 2.41 48.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.304 α = 90 b = 69.304 β = 90 c = 166.644 γ = 90
Symmetry Space Group P 43 21 2
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+ osmic mirrors 2014-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54187
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.909 29 95.2 0.096 0.098 0.02 0.999 12.5 20.7 30956 28.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.909 1.93 84.6 0.673 0.768 0.355 0.647 1.6 3.9
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 6C76 1.91 29 28792 1997 94.83 0.14011 0.13668 0.1397 0.18939 0.1911 RANDOM 42.895
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] 0.13 0.13 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.225 r_dihedral_angle_4_deg 19.779 r_dihedral_angle_3_deg 16.118 r_long_range_B_refined 9.389 r_long_range_B_other 9.388 r_dihedral_angle_1_deg 6.258 r_scangle_it 5.235 r_scangle_other 5.234 r_scbond_it 3.425 r_scbond_other 3.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.225 r_dihedral_angle_4_deg 19.779 r_dihedral_angle_3_deg 16.118 r_long_range_B_refined 9.389 r_long_range_B_other 9.388 r_dihedral_angle_1_deg 6.258 r_scangle_it 5.235 r_scangle_other 5.234 r_scbond_it 3.425 r_scbond_other 3.424 r_mcangle_other 3.034 r_mcangle_it 3.033 r_mcbond_it 2.222 r_mcbond_other 2.22 r_angle_refined_deg 1.122 r_angle_other_deg 0.679 r_symmetry_vdw_refined 0.278 r_nbd_refined 0.247 r_nbtor_refined 0.185 r_symmetry_vdw_other 0.174 r_nbd_other 0.172 r_symmetry_hbond_refined 0.14 r_xyhbond_nbd_refined 0.119 r_nbtor_other 0.084 r_chiral_restr 0.075 r_xyhbond_nbd_other 0.045 r_gen_planes_refined 0.012 r_bond_refined_d 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_metal_ion_refined r_metal_ion_other 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 2926 Nucleic Acid Atoms Solvent Atoms 462 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing