5VKR

Horse liver alcohol dehydrogenase complexed with adenosine-5-diphosphoribose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS8.427810 mg/ml protein in dialysis bag dialyzed against 50 mM Tris-HCl, pH 8.4 as the concentration of 2-methyl-2,4-pentanediol was raised to 25 %. A crystal was soaked with 2 mM adenosine-5-diphosphoribose in the final outer dialysate for 1 hr. Crystal flash vitrified by plunging it into liquid N2.
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.37α = 90
b = 74.27β = 90
c = 180.95γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Si(111)2001-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1.0093APS19-ID

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
11.82091.70.11797.643081643.6
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)
11.81.8684.80.5072.15.68

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 REPLACEMENTTHROUGHOUT8ADH1.82030816132891.680.192330.190010.24775RANDOM50.595
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]
0.183.2-3.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.311
r_dihedral_angle_4_deg19.867
r_dihedral_angle_3_deg16.82
r_long_range_B_refined11.44
r_long_range_B_other11.431
r_scangle_other9.798
r_dihedral_angle_1_deg6.737
r_scbond_it6.475
r_scbond_other6.474
r_mcangle_other5.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.311
r_dihedral_angle_4_deg19.867
r_dihedral_angle_3_deg16.82
r_long_range_B_refined11.44
r_long_range_B_other11.431
r_scangle_other9.798
r_dihedral_angle_1_deg6.737
r_scbond_it6.475
r_scbond_other6.474
r_mcangle_other5.58
r_mcangle_it5.564
r_mcbond_it4.164
r_mcbond_other4.113
r_angle_refined_deg2.066
r_angle_other_deg1.086
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.01
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2785
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms38

Software

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