4NFS

V203A horse liver alcohol dehydrogenase E complexed with NAD and 2,2,2-trifluoroethanol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DXHPDB ENTRY 4DXH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS727850 mN ammonium N-[tris(hydroxymethyl)methyl]-2-amminoethanesulfonate and 0.5 mM EDTA, pH 6.7 (at 25 deg C), 10 mg/ml protein, 1 mM NAD+, 100 mM 2,2,2-trifluoroethanol, 13-25 % 2-methyl-2,4-methylpentanediol, MICRODIALYSIS, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.448.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.28α = 91.88
b = 51.41β = 103.09
c = 92.53γ = 109.94
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-1Rosenbaum-Rock vertically focussed mirrors2007-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.20.802ALS4.2.2

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
11.12088.30.04112.23.0531030826612311.9
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)
11.11.1450.60.3852.22.9115266

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4DXH1.119.58263388269088.310.137810.137430.17474RANDOM17.884
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]
0.04-0.08-0.020.21-0.34-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free53.322
r_dihedral_angle_2_deg38.071
r_sphericity_bonded13.932
r_dihedral_angle_4_deg13.355
r_rigid_bond_restr12.098
r_dihedral_angle_3_deg11.105
r_dihedral_angle_1_deg6.256
r_long_range_B_refined5.868
r_long_range_B_other4.218
r_scangle_other3.338
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free53.322
r_dihedral_angle_2_deg38.071
r_sphericity_bonded13.932
r_dihedral_angle_4_deg13.355
r_rigid_bond_restr12.098
r_dihedral_angle_3_deg11.105
r_dihedral_angle_1_deg6.256
r_long_range_B_refined5.868
r_long_range_B_other4.218
r_scangle_other3.338
r_scbond_other3.171
r_scbond_it3.17
r_angle_refined_deg1.933
r_mcangle_it1.755
r_mcangle_other1.755
r_mcbond_it1.657
r_mcbond_other1.657
r_angle_other_deg0.927
r_chiral_restr0.121
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5566
Nucleic Acid Atoms
Solvent Atoms1034
Heterogen Atoms136

Software

Software
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling