2QR9

Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed with an Oxabicyclic Derivative Compound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ERDPDB entry 3ERD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52980.1M Tris 8.5, 0.2M Magnesium Hexahydrate, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1141.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.987α = 90
b = 84.002β = 108.85
c = 58.724γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2007-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97946SSRLBL11-1

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
121089.40.0620.06218.654310553105528.72
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)
122.0792.20.1560.15610.6543192

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3ERD2102942930981155289.070.2160.2140.262RANDOM17.465
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]
-1.79-0.352.89-1.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.149
r_dihedral_angle_4_deg21.541
r_dihedral_angle_3_deg17.053
r_dihedral_angle_1_deg5.797
r_scangle_it2.994
r_scbond_it1.933
r_angle_refined_deg1.546
r_mcangle_it1.315
r_angle_other_deg0.992
r_mcbond_it0.838
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.149
r_dihedral_angle_4_deg21.541
r_dihedral_angle_3_deg17.053
r_dihedral_angle_1_deg5.797
r_scangle_it2.994
r_scbond_it1.933
r_angle_refined_deg1.546
r_mcangle_it1.315
r_angle_other_deg0.992
r_mcbond_it0.838
r_symmetry_vdw_other0.272
r_nbd_refined0.229
r_xyhbond_nbd_refined0.204
r_nbd_other0.187
r_symmetry_hbond_refined0.182
r_nbtor_refined0.178
r_symmetry_vdw_refined0.174
r_mcbond_other0.171
r_nbtor_other0.091
r_chiral_restr0.083
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3978
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms58

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling