2QH6 | pdb_00002qh6

Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed with an Oxabicyclic diarylethylene Compound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ERD	PDB entry 3ERD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.02	39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.765	α = 90
b = 81.718	β = 109.9
c = 58.31	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315	bent conical Si-mirror (Rh coating)	2004-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9734	APS	14-BM-C

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.7	20	97.8	0.113	0.113	14.8	3.5	13294	13294			17.36

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)	Redundancy	Number Unique Reflections (All)
1	2.7	2.8	98.7		0.546	0.546	3.47	3.4	1332

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3ERD	2.7	19.73	13275	13275	691	97.74	0.209	0.205	0.2	0.291	0.29	RANDOM	17.364

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]
-2.11		-0.56	4.93		-3.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.287
r_dihedral_angle_4_deg	29.452
r_dihedral_angle_3_deg	20.918
r_dihedral_angle_1_deg	6.179
r_scangle_it	5.372
r_scbond_it	3.598
r_mcangle_it	2.444
r_angle_refined_deg	1.92
r_mcbond_it	1.665
r_nbtor_refined	0.322

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.287
r_dihedral_angle_4_deg	29.452
r_dihedral_angle_3_deg	20.918
r_dihedral_angle_1_deg	6.179
r_scangle_it	5.372
r_scbond_it	3.598
r_mcangle_it	2.444
r_angle_refined_deg	1.92
r_mcbond_it	1.665
r_nbtor_refined	0.322
r_symmetry_vdw_refined	0.291
r_nbd_refined	0.268
r_symmetry_hbond_refined	0.243
r_chiral_restr	0.212
r_xyhbond_nbd_refined	0.17
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3845
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	62

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.