6C75

Structure of Iron containing alcohol dehydrogenase from Thermococcus thioreducens in a monoclinic crystal form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O2D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52980.1 M Sodium acetate, 8% PEG 4000, pH 4.5
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.125α = 90
b = 99.248β = 103.16
c = 67.487γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRIGAKU SATURN 944+Osmic mirrors2013-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54187

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.449.61790.2340.2530.0920.982126.52338548.6
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)RedundancyNumber Unique Reflections (All)
12.42.49220.7490.9930.6460.3681.81.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1O2D2.449.6122218115078.880.146360.143110.2081RANDOM66.1
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]
1.62.47-0.5-2.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.97
r_dihedral_angle_4_deg20.353
r_dihedral_angle_3_deg18.673
r_long_range_B_other9.807
r_long_range_B_refined9.804
r_dihedral_angle_1_deg7.983
r_scangle_it7.514
r_scangle_other7.508
r_mcangle_it5.413
r_mcangle_other5.412
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.97
r_dihedral_angle_4_deg20.353
r_dihedral_angle_3_deg18.673
r_long_range_B_other9.807
r_long_range_B_refined9.804
r_dihedral_angle_1_deg7.983
r_scangle_it7.514
r_scangle_other7.508
r_mcangle_it5.413
r_mcangle_other5.412
r_scbond_it4.706
r_scbond_other4.701
r_mcbond_it3.603
r_mcbond_other3.603
r_angle_refined_deg0.615
r_angle_other_deg0.496
r_symmetry_vdw_refined0.266
r_symmetry_vdw_other0.231
r_nbd_refined0.221
r_nbd_other0.208
r_nbtor_refined0.188
r_xyhbond_nbd_refined0.141
r_nbtor_other0.093
r_symmetry_hbond_refined0.085
r_chiral_restr0.04
r_xyhbond_nbd_other0.034
r_gen_planes_refined0.012
r_bond_refined_d0.003
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms5852
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing