2QZO

Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed with WAY-169916


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52980.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0439.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.806α = 90
b = 82.029β = 109.04
c = 58.517γ = 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
11.721595.40.0460.04627.94.74827630.73
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)
11.721.8682.10.1760.1766.573.43762

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 DIFFRACTIONTHROUGHOUTPDB entry 3ERD1.729.914812448124244691.580.180.1780.221RANDOM17.541
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]
-0.05-0.02-0.010.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.345
r_dihedral_angle_4_deg23.794
r_dihedral_angle_3_deg15.49
r_dihedral_angle_1_deg8.04
r_scangle_it3.65
r_scbond_it2.504
r_mcangle_it1.508
r_angle_refined_deg1.489
r_angle_other_deg0.993
r_mcbond_it0.991
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.345
r_dihedral_angle_4_deg23.794
r_dihedral_angle_3_deg15.49
r_dihedral_angle_1_deg8.04
r_scangle_it3.65
r_scbond_it2.504
r_mcangle_it1.508
r_angle_refined_deg1.489
r_angle_other_deg0.993
r_mcbond_it0.991
r_symmetry_vdw_refined0.533
r_symmetry_hbond_refined0.383
r_symmetry_vdw_other0.334
r_mcbond_other0.241
r_nbd_refined0.238
r_nbd_other0.211
r_xyhbond_nbd_refined0.188
r_nbtor_refined0.183
r_chiral_restr0.151
r_nbtor_other0.112
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3816
Nucleic Acid Atoms
Solvent Atoms422
Heterogen Atoms48

Software

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