2ZKC

Crystal structure of human estrogen-related receptor gamma ligand binding domain complex with bisphenol Z


X-RAY DIFFRACTION

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 293K
Crystal Properties
Matthews coefficientSolvent content
2.5150.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.839α = 90
b = 63.839β = 90
c = 135.894γ = 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
11.731.9399.90.070.0748.67.531736
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)
11.71.761000.4730.4733.47.15929

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 2E2R1.731.0730138159999.790.19920.197440.23362RANDOM26.478
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.554
r_dihedral_angle_4_deg15.465
r_dihedral_angle_3_deg13.57
r_dihedral_angle_1_deg4.654
r_scangle_it3.507
r_scbond_it2.281
r_mcangle_it1.53
r_angle_refined_deg1.368
r_mcbond_it0.991
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.554
r_dihedral_angle_4_deg15.465
r_dihedral_angle_3_deg13.57
r_dihedral_angle_1_deg4.654
r_scangle_it3.507
r_scbond_it2.281
r_mcangle_it1.53
r_angle_refined_deg1.368
r_mcbond_it0.991
r_nbtor_refined0.309
r_nbd_refined0.236
r_symmetry_hbond_refined0.178
r_symmetry_vdw_refined0.142
r_xyhbond_nbd_refined0.141
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1799
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms32

Software

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