2QGT

Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed to an Ether Estradiol 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 DROP8298VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.0941.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.171α = 90
b = 83.708β = 108.45
c = 56.007γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-3mirrors2004-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97945APS19-BM

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
12.155098.70.1180.1184.13.7283012830120.43
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)
12.152.2395.70.3950.3951.83.12736

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 3ERD2.15202825128251143196.930.1940.1920.24RANDOM16.469
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]
0.12-0.07-0.07-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.744
r_dihedral_angle_3_deg16.386
r_dihedral_angle_4_deg15.846
r_dihedral_angle_1_deg4.853
r_scangle_it2.747
r_scbond_it1.931
r_mcangle_it1.471
r_angle_refined_deg1.149
r_mcbond_it0.986
r_angle_other_deg0.914
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.744
r_dihedral_angle_3_deg16.386
r_dihedral_angle_4_deg15.846
r_dihedral_angle_1_deg4.853
r_scangle_it2.747
r_scbond_it1.931
r_mcangle_it1.471
r_angle_refined_deg1.149
r_mcbond_it0.986
r_angle_other_deg0.914
r_symmetry_vdw_other0.336
r_symmetry_vdw_refined0.288
r_nbd_refined0.209
r_nbd_other0.197
r_xyhbond_nbd_refined0.19
r_symmetry_hbond_refined0.179
r_nbtor_refined0.174
r_mcbond_other0.173
r_nbtor_other0.088
r_chiral_restr0.071
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3978
Nucleic Acid Atoms
Solvent Atoms134
Heterogen Atoms46

Software

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