2JHG

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 1HETPDB ENTRY 1HET

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 = 50.186α = 77.12
b = 43.798β = 87.44
c = 92.516γ = 108.89
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
11.22594.10.0517.82.6212570
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)
11.21.2389.10.222.82

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 1HET1.219.832099202129940.1150.1140.142RANDOM13.31
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]
0.27-0.04-0.040.01-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.811
r_dihedral_angle_3_deg12.87
r_dihedral_angle_4_deg12.407
r_dihedral_angle_1_deg6.219
r_scangle_it4.144
r_scbond_it3.289
r_mcangle_it2.36
r_mcbond_it1.983
r_angle_refined_deg1.929
r_angle_other_deg1.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.811
r_dihedral_angle_3_deg12.87
r_dihedral_angle_4_deg12.407
r_dihedral_angle_1_deg6.219
r_scangle_it4.144
r_scbond_it3.289
r_mcangle_it2.36
r_mcbond_it1.983
r_angle_refined_deg1.929
r_angle_other_deg1.094
r_nbd_refined0.267
r_symmetry_vdw_other0.234
r_symmetry_hbond_refined0.228
r_nbd_other0.21
r_xyhbond_nbd_refined0.202
r_chiral_restr0.195
r_nbtor_refined0.185
r_symmetry_vdw_refined0.174
r_nbtor_other0.114
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms1236
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling