2QXM

Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed to Burned Meat Compound PhIP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.52980.2M Magnesium chloride hexahydrate, 0.1M Tris 8.5, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.0941.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.965α = 90
b = 83.703β = 108.7
c = 58.427γ = 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 BL11-1SSRLBL11-1

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
12.31288.80.120.1216.73.32019946.85
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)
12.32.3886.90.2410.2413.733

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 3ERD2.311.962013820138104088.50.2740.2730.296RANDOM26.26
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]
-0.26-0.34-0.450.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.002
r_dihedral_angle_4_deg23.685
r_dihedral_angle_3_deg18.729
r_scangle_it15.056
r_scbond_it14.837
r_mcangle_it11.031
r_mcbond_it10.175
r_dihedral_angle_1_deg6.294
r_angle_other_deg2.739
r_angle_refined_deg1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.002
r_dihedral_angle_4_deg23.685
r_dihedral_angle_3_deg18.729
r_scangle_it15.056
r_scbond_it14.837
r_mcangle_it11.031
r_mcbond_it10.175
r_dihedral_angle_1_deg6.294
r_angle_other_deg2.739
r_angle_refined_deg1.54
r_mcbond_other1.367
r_symmetry_hbond_refined1.098
r_symmetry_vdw_other0.401
r_symmetry_vdw_refined0.268
r_nbd_other0.256
r_nbd_refined0.24
r_nbtor_refined0.195
r_xyhbond_nbd_refined0.149
r_nbtor_other0.1
r_chiral_restr0.093
r_xyhbond_nbd_other0.048
r_bond_refined_d0.018
r_bond_other_d0.01
r_gen_planes_other0.009
r_gen_planes_refined0.006
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3927
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms34

Software

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