2JHF

Structural evidence for a ligand coordination switch in liver alcohol dehydrogenase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HEUPDB ENTRY 1HEU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1DIALYSIS 30 MM TRIS/HCL PH 8.2 25 % MPD
Crystal Properties
Matthews coefficientSolvent content
2.245

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.87α = 104.4
b = 44.46β = 101.4
c = 94.18γ = 71.1
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

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
1125800.0416.71.7323884
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)
111.0367.50.441.41.3

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 1HEU120322228161379.90.1250.1250.152RANDOM12.8
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]
0.371.490.15-0.01-0.05-1.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.009
r_dihedral_angle_4_deg14.658
r_dihedral_angle_3_deg12.66
r_dihedral_angle_1_deg6.292
r_scangle_it5.46
r_scbond_it4.34
r_angle_other_deg3.29
r_mcbond_it3.136
r_mcangle_it3.131
r_angle_refined_deg2.207
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.009
r_dihedral_angle_4_deg14.658
r_dihedral_angle_3_deg12.66
r_dihedral_angle_1_deg6.292
r_scangle_it5.46
r_scbond_it4.34
r_angle_other_deg3.29
r_mcbond_it3.136
r_mcangle_it3.131
r_angle_refined_deg2.207
r_chiral_restr0.305
r_nbd_refined0.243
r_symmetry_hbond_refined0.243
r_symmetry_vdw_refined0.234
r_symmetry_vdw_other0.226
r_nbd_other0.225
r_xyhbond_nbd_refined0.189
r_nbtor_refined0.164
r_nbtor_other0.095
r_gen_planes_other0.032
r_bond_refined_d0.026
r_gen_planes_refined0.013
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5570
Nucleic Acid Atoms
Solvent Atoms1241
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing