☰ Navigation Tabs
Structure of Iron containing alcohol dehydrogenase from Thermococcus thioreducens in a monoclinic crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O2D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 298 0.1 M Sodium acetate, 8% PEG 4000, pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.125 α = 90 b = 99.248 β = 103.16 c = 67.487 γ = 90
Symmetry Space Group P 1 21 1
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 2013-04-11 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 2.4 49.61 79 0.234 0.253 0.092 0.982 12 6.5 23385 48.6
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 2.4 2.49 22 0.749 0.993 0.646 0.368 1.8 1.7
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 1O2D 2.4 49.61 22218 1150 78.88 0.14636 0.14311 0.142 0.2081 0.2086 RANDOM 66.1
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] 1.6 2.47 -0.5 -2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.97 r_dihedral_angle_4_deg 20.353 r_dihedral_angle_3_deg 18.673 r_long_range_B_other 9.807 r_long_range_B_refined 9.804 r_dihedral_angle_1_deg 7.983 r_scangle_it 7.514 r_scangle_other 7.508 r_mcangle_it 5.413 r_mcangle_other 5.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.97 r_dihedral_angle_4_deg 20.353 r_dihedral_angle_3_deg 18.673 r_long_range_B_other 9.807 r_long_range_B_refined 9.804 r_dihedral_angle_1_deg 7.983 r_scangle_it 7.514 r_scangle_other 7.508 r_mcangle_it 5.413 r_mcangle_other 5.412 r_scbond_it 4.706 r_scbond_other 4.701 r_mcbond_it 3.603 r_mcbond_other 3.603 r_angle_refined_deg 0.615 r_angle_other_deg 0.496 r_symmetry_vdw_refined 0.266 r_symmetry_vdw_other 0.231 r_nbd_refined 0.221 r_nbd_other 0.208 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.141 r_nbtor_other 0.093 r_symmetry_hbond_refined 0.085 r_chiral_restr 0.04 r_xyhbond_nbd_other 0.034 r_gen_planes_refined 0.012 r_bond_refined_d 0.003 r_gen_planes_other 0.002 r_bond_other_d 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 5852 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing