2ZAS

Crystal structure of human estrogen-related receptor gamma ligand binding domain complex with 4-alpha-cumylphenol, a bisphenol A derivative


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E2RPDB ENTRY 2E2R

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.05M HEPES, 0.75M sodium citrate, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.5351.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.018α = 90
b = 64.018β = 90
c = 136.197γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
1237.899.40.1230.123156.61991919919
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0799.50.7050.7051.46.31948

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2E2R237.81886218862101599.470.212260.212260.210950.23676RANDOM28.056
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.533
r_dihedral_angle_4_deg16.33
r_dihedral_angle_3_deg13.718
r_dihedral_angle_1_deg4.839
r_scangle_it2.268
r_scbond_it1.495
r_angle_refined_deg1.145
r_mcangle_it1.071
r_mcbond_it0.699
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.533
r_dihedral_angle_4_deg16.33
r_dihedral_angle_3_deg13.718
r_dihedral_angle_1_deg4.839
r_scangle_it2.268
r_scbond_it1.495
r_angle_refined_deg1.145
r_mcangle_it1.071
r_mcbond_it0.699
r_nbtor_refined0.298
r_nbd_refined0.198
r_symmetry_vdw_refined0.137
r_symmetry_hbond_refined0.127
r_xyhbond_nbd_refined0.114
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1805
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing