2QSE

Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain complexed with Burned Meat Compound 4-OH-PhIP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52980.2M Magnesium chloride hexahydrate, 0.1M Tris 8.5, 25% Polyehtlyene glycol 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1141.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.081α = 90
b = 84.044β = 108.85
c = 58.668γ = 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
11.851595.10.0640.06417.54.3417924179233.7
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)
11.851.9271.20.2830.2833.682.53122

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 3ERD1.8514.9941769417692117950.1710.1690.225RANDOM21.827
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]
-0.020.01-0.010.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.306
r_dihedral_angle_4_deg22.726
r_dihedral_angle_3_deg15.895
r_dihedral_angle_1_deg5.359
r_scangle_it3.328
r_scbond_it2.171
r_mcangle_it1.503
r_angle_refined_deg1.422
r_mcbond_it0.988
r_angle_other_deg0.957
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.306
r_dihedral_angle_4_deg22.726
r_dihedral_angle_3_deg15.895
r_dihedral_angle_1_deg5.359
r_scangle_it3.328
r_scbond_it2.171
r_mcangle_it1.503
r_angle_refined_deg1.422
r_mcbond_it0.988
r_angle_other_deg0.957
r_symmetry_vdw_refined0.33
r_symmetry_vdw_other0.289
r_symmetry_hbond_refined0.248
r_nbd_refined0.24
r_mcbond_other0.213
r_nbd_other0.194
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.18
r_nbtor_other0.091
r_chiral_restr0.082
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3944
Nucleic Acid Atoms
Solvent Atoms359
Heterogen Atoms36

Software

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