5KJ6

V197I Horse liver alcohol dehydrogenase complexed with NAD+ and pentafluorobenzyl alcohol


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-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA, 10 MG/ML PROTEIN, 1 MM NAD+, 19 MM 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL
Crystal Properties
Matthews coefficientSolvent content
2.2646

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.47α = 91.92
b = 51.65β = 103.01
c = 92.68γ = 110.17
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-12008-01-01MSINGLE 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
11.1420860.04714.83.432348009.9
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)
11.141.1851.10.3842.33.2

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 REPLACEMENTTHROUGHOUT4DWV1.1420233565117285.920.136540.13640.16415RANDOM17.159
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]
0.3-0.270.340.270.24-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.197
r_sphericity_free29.932
r_dihedral_angle_4_deg14.03
r_dihedral_angle_3_deg11.66
r_sphericity_bonded8.54
r_dihedral_angle_1_deg6.331
r_rigid_bond_restr4.87
r_long_range_B_refined3.593
r_long_range_B_other2.901
r_scangle_other2.701
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.197
r_sphericity_free29.932
r_dihedral_angle_4_deg14.03
r_dihedral_angle_3_deg11.66
r_sphericity_bonded8.54
r_dihedral_angle_1_deg6.331
r_rigid_bond_restr4.87
r_long_range_B_refined3.593
r_long_range_B_other2.901
r_scangle_other2.701
r_scbond_other2.457
r_scbond_it2.453
r_angle_refined_deg2.194
r_mcangle_it1.638
r_mcangle_other1.637
r_angle_other_deg1.517
r_mcbond_it1.433
r_mcbond_other1.433
r_chiral_restr0.131
r_bond_refined_d0.021
r_gen_planes_refined0.011
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 Atoms973
Heterogen Atoms150

Software

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