2W4Q

Crystal structure of human zinc-binding alcohol dehydrogenase 1 (ZADH1) in ternary complex with NADP and 18beta-glycyrrhetinic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VNAPDB ENTRY 2VNA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M TRIS PH 8.5; 2M (NH4)2SO4
Crystal Properties
Matthews coefficientSolvent content
2.5551.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.374α = 90
b = 84.11β = 109.05
c = 72.888γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEOSMIC2008-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
1268.9990.14253012

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 2VNA268.8425301134199.40.180.1770.223RANDOM15.72
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]
-0.06-0.110.29-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.285
r_dihedral_angle_4_deg12.684
r_dihedral_angle_3_deg12.145
r_scangle_it6.737
r_dihedral_angle_1_deg5.767
r_scbond_it5.118
r_mcangle_it2.913
r_mcbond_it1.878
r_angle_refined_deg1.413
r_angle_other_deg0.835
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.285
r_dihedral_angle_4_deg12.684
r_dihedral_angle_3_deg12.145
r_scangle_it6.737
r_dihedral_angle_1_deg5.767
r_scbond_it5.118
r_mcangle_it2.913
r_mcbond_it1.878
r_angle_refined_deg1.413
r_angle_other_deg0.835
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 Atoms2652
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing