2E2R

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S9QPDB ENTRY 1S9Q

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
2.5451.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.046α = 90
b = 64.046β = 90
c = 136.871γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102006-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.00SPring-8BL38B1

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
11.628.0699.60.0580.05840.411.93641436414
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)
11.61.6699.20.3490.3498.211.33729

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 1S9Q1.628.063641436414192199.610.170710.170710.169340.19666RANDOM16.709
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_1_deg5.123
r_scangle_it3.479
r_scbond_it2.116
r_mcangle_it1.336
r_angle_refined_deg1.333
r_angle_other_deg0.822
r_mcbond_it0.714
r_symmetry_vdw_other0.245
r_nbd_other0.228
r_nbd_refined0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.123
r_scangle_it3.479
r_scbond_it2.116
r_mcangle_it1.336
r_angle_refined_deg1.333
r_angle_other_deg0.822
r_mcbond_it0.714
r_symmetry_vdw_other0.245
r_nbd_other0.228
r_nbd_refined0.22
r_symmetry_hbond_refined0.208
r_xyhbond_nbd_refined0.154
r_symmetry_vdw_refined0.124
r_nbtor_other0.085
r_chiral_restr0.075
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_gen_planes_other0.006
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1806
Nucleic Acid Atoms
Solvent Atoms387
Heterogen Atoms35

Software

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