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Structure of Iron containing alcohol dehydrogenase from Thermococcus thioreducens in an orthorhombic crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C75
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 0.1 M sodium acetate, 10% PEG 10,000 at pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.34 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.92 α = 90 b = 111.978 β = 90 c = 142.081 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD RIGAKU SATURN 944+ OSMIC MIRRORS 2013-04-18 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 2.1 43.97 90 0.209 0.214 0.041 0.995 13 20.4 41831 36.7
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 2.1 2.16 35.6 0.974 1.192 0.67 0.222 0.7 2.4
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 6C75 2.1 33.04 39750 2018 89.82 0.15633 0.15387 0.1535 0.20419 0.2041 RANDOM 46.619
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] -0.03 0.98 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.979 r_dihedral_angle_4_deg 23.011 r_dihedral_angle_3_deg 18.033 r_long_range_B_refined 10.5 r_long_range_B_other 10.478 r_scangle_it 7.737 r_scangle_other 7.737 r_dihedral_angle_1_deg 7.442 r_mcangle_other 4.997 r_mcangle_it 4.995
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.979 r_dihedral_angle_4_deg 23.011 r_dihedral_angle_3_deg 18.033 r_long_range_B_refined 10.5 r_long_range_B_other 10.478 r_scangle_it 7.737 r_scangle_other 7.737 r_dihedral_angle_1_deg 7.442 r_mcangle_other 4.997 r_mcangle_it 4.995 r_scbond_it 4.862 r_scbond_other 4.862 r_mcbond_it 3.46 r_mcbond_other 3.453 r_angle_refined_deg 0.964 r_angle_other_deg 0.618 r_symmetry_vdw_refined 0.294 r_symmetry_hbond_refined 0.288 r_symmetry_vdw_other 0.266 r_nbd_refined 0.235 r_nbd_other 0.199 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.134 r_nbtor_other 0.089 r_symmetry_hbond_other 0.088 r_chiral_restr 0.061 r_xyhbond_nbd_other 0.054 r_gen_planes_refined 0.017 r_bond_refined_d 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.003 r_metal_ion_refined r_metal_ion_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 5852 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing