5KCZ

horse liver S48T alcohol dehydrogenase complexed with NAD and trifluoroethanol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DWV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS727850 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminomethane sulfonate, pH 7.0 (pH 6.7 at 25 C), 0.25 mM EDTA, 10 mg/ml protein, 1 mM NAD+, 100 mM trifluoroethanol, 12-25 % 2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
2.2646

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.4α = 91.97
b = 51.38β = 103.03
c = 92.29γ = 110.28
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-12008-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.20.827ALS4.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.142090.70.04713.83.722448469.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.141.1754.60.3723.2

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 REPLACEMENTTHROUGHOUT4DWV1.1420243550120690.680.126130.126020.14788RANDOM14.897
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]
0.25-0.370.220.52-0.02-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.517
r_sphericity_free23.844
r_dihedral_angle_4_deg15.33
r_dihedral_angle_3_deg10.85
r_sphericity_bonded6.627
r_dihedral_angle_1_deg6.255
r_rigid_bond_restr3.183
r_long_range_B_refined3.01
r_long_range_B_other2.262
r_angle_refined_deg1.839
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.517
r_sphericity_free23.844
r_dihedral_angle_4_deg15.33
r_dihedral_angle_3_deg10.85
r_sphericity_bonded6.627
r_dihedral_angle_1_deg6.255
r_rigid_bond_restr3.183
r_long_range_B_refined3.01
r_long_range_B_other2.262
r_angle_refined_deg1.839
r_scangle_other1.792
r_scbond_it1.581
r_scbond_other1.581
r_mcangle_it1.194
r_mcangle_other1.194
r_angle_other_deg1.016
r_mcbond_it0.979
r_mcbond_other0.978
r_chiral_restr0.108
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5572
Nucleic Acid Atoms
Solvent Atoms1028
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
REFMACphasing