5VJG

horse liver alcohol dehydrogenase complexed with 2,2'bipyridine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8ADH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS8.4278Dialysis of 10 mg protein/ml against 50 mM Tris-HCl, pH 8.4, as the concentration of 2-methyl-2,4-pentanediol concentration was raised to 25 %. Crysta was soaked for 3 hr iwth 30 mM 2,2'-bipyridine before flash vitrification with liquid N2.l
Crystal Properties
Matthews coefficientSolvent content
2.3247.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.45α = 90
b = 73.7β = 90
c = 181.14γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++MSC Yale confocal osmic2005-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
11.92095.30.1189.86.992714829.2
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)
11.91.9787.40.3423.55.04

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 REPLACEMENTTHROUGHOUT8ADH1.92027148117495.280.20750.20440.2836RANDOM41.412
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]
2.420.91-3.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.471
r_dihedral_angle_4_deg19.96
r_dihedral_angle_3_deg16.011
r_dihedral_angle_1_deg7.013
r_angle_refined_deg1.804
r_angle_other_deg1.043
r_chiral_restr0.1
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.471
r_dihedral_angle_4_deg19.96
r_dihedral_angle_3_deg16.011
r_dihedral_angle_1_deg7.013
r_angle_refined_deg1.804
r_angle_other_deg1.043
r_chiral_restr0.1
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2785
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms14

Software

Software
Software NamePurpose
d*TREKdata reduction
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Omodel building
MOLREPphasing