7XWR

Human Estrogen Receptor beta Ligand-binding Domain in Complex with (S)-2-(2-chloro-4-hydroxyphenyl)-3-(4-hydroxyphenyl)propanenitrile


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GIU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529316-20% PEG3350, 100 mM BisTris pH6.5, 200 mM Magnesium Acetate
Crystal Properties
Matthews coefficientSolvent content
2.0439.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.436α = 90
b = 89.226β = 90
c = 101.532γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.0Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.1646.63399.30.4510.5370.2880.9374.45.925917
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.162.232.1862.6641.4990.6235.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2giu2.16446.63325840129498.9550.2640.26140.3178RANDOM26.142
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]
3.579-9.3835.804
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.882
r_dihedral_angle_3_deg16.102
r_dihedral_angle_4_deg15.571
r_dihedral_angle_1_deg6.291
r_lrange_it5.798
r_lrange_other5.798
r_scangle_it3.937
r_scangle_other3.936
r_mcangle_it3.581
r_mcangle_other3.581
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.882
r_dihedral_angle_3_deg16.102
r_dihedral_angle_4_deg15.571
r_dihedral_angle_1_deg6.291
r_lrange_it5.798
r_lrange_other5.798
r_scangle_it3.937
r_scangle_other3.936
r_mcangle_it3.581
r_mcangle_other3.581
r_scbond_it2.432
r_scbond_other2.432
r_mcbond_it2.245
r_mcbond_other2.244
r_angle_refined_deg1.555
r_angle_other_deg1.289
r_symmetry_xyhbond_nbd_refined0.501
r_symmetry_nbd_refined0.293
r_nbd_other0.263
r_nbd_refined0.222
r_xyhbond_nbd_refined0.183
r_symmetry_nbd_other0.171
r_nbtor_refined0.16
r_symmetry_nbtor_other0.081
r_chiral_restr0.068
r_symmetry_xyhbond_nbd_other0.038
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3530
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing