5KJF

V222I horse liver alcohol dehydrogenase complexed with NAD+ and trifluoroethanol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5KJC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS727850 MM AMMONIUM N-[TRIS(HYDROXYMETHYL) METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA, 10 MG/ML PROTEIN, 1 MM NAD+, 100 MM 2,2,2-TRIFLUOROETHANOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL
Crystal Properties
Matthews coefficientSolvent content
2.2646

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.2α = 91.88
b = 51.33β = 103.06
c = 92.53γ = 109.84
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-12008-12-04MSINGLE 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
11.22088.30.05111.13.6320433412.7
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)
11.21.2464.60.4041.93.57

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 REPLACEMENTTHROUGHOUT5KJC1.220202264207088.280.133020.132820.15312RANDOM18.113
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]
0.44-0.080.410.34-0.13-0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.825
r_sphericity_free28.252
r_dihedral_angle_4_deg12.855
r_dihedral_angle_3_deg11.456
r_sphericity_bonded8.315
r_dihedral_angle_1_deg6.139
r_long_range_B_refined3.482
r_long_range_B_other2.675
r_scangle_other2.324
r_rigid_bond_restr2.195
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.825
r_sphericity_free28.252
r_dihedral_angle_4_deg12.855
r_dihedral_angle_3_deg11.456
r_sphericity_bonded8.315
r_dihedral_angle_1_deg6.139
r_long_range_B_refined3.482
r_long_range_B_other2.675
r_scangle_other2.324
r_rigid_bond_restr2.195
r_scbond_other2.002
r_scbond_it2.001
r_angle_refined_deg1.792
r_mcangle_other1.417
r_mcangle_it1.416
r_mcbond_it1.21
r_mcbond_other1.209
r_angle_other_deg1.013
r_chiral_restr0.109
r_bond_refined_d0.014
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 Atoms912
Heterogen Atoms144

Software

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