2QGW

Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed with a Chloro-Indazole 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 DROP298VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.141.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.053α = 90
b = 84.266β = 108.48
c = 58.213γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBCmirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97934APS19-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
12.355095.70.0970.0974.73.8209382093830.69
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)
12.352.4393.60.4150.4151.83.22028

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 3ERD2.3933.37179131791392087.460.2410.2380.296RANDOM24.294
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]
0.641.030.41-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.83
r_dihedral_angle_4_deg18.369
r_dihedral_angle_3_deg16.721
r_dihedral_angle_1_deg5.167
r_scangle_it1.613
r_angle_refined_deg1.341
r_scbond_it1.134
r_angle_other_deg1.025
r_mcangle_it0.972
r_mcbond_it0.881
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.83
r_dihedral_angle_4_deg18.369
r_dihedral_angle_3_deg16.721
r_dihedral_angle_1_deg5.167
r_scangle_it1.613
r_angle_refined_deg1.341
r_scbond_it1.134
r_angle_other_deg1.025
r_mcangle_it0.972
r_mcbond_it0.881
r_xyhbond_nbd_refined0.67
r_symmetry_vdw_refined0.462
r_symmetry_vdw_other0.289
r_nbd_refined0.206
r_nbd_other0.194
r_nbtor_refined0.171
r_symmetry_hbond_refined0.134
r_chiral_restr0.105
r_mcbond_other0.101
r_nbtor_other0.088
r_bond_refined_d0.01
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3982
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms36

Software

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