2P15 | pdb_00002p15

Crystal structure of the ER alpha ligand binding domain with the agonist ortho-trifluoromethylphenylvinyl estradiol

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	20% PEG 4000, 0.2M Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.052	α = 90
b = 84.22	β = 109.59
c = 58.693	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	SBC-2	SI 111 MONOCHROMATOR	2004-08-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID

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	1.87	50	92.4	0.08	0.08	6.6	4.7	39661	39661			20.061

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	1.87	1.94	55.2		0.395	0.395	1.738	3	2369

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.94	27.71	36913	36913	1871	96.99	0.161	0.161	0.158	0.16	0.216	0.21	RANDOM	20.061

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]
-0.08		-0.01	0.12		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.211
r_dihedral_angle_4_deg	22.581
r_dihedral_angle_3_deg	14.976
r_dihedral_angle_1_deg	5.005
r_scangle_it	3.14
r_scbond_it	2.164
r_angle_refined_deg	1.358
r_mcangle_it	1.194
r_mcbond_it	1.003
r_symmetry_hbond_refined	0.409

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.211
r_dihedral_angle_4_deg	22.581
r_dihedral_angle_3_deg	14.976
r_dihedral_angle_1_deg	5.005
r_scangle_it	3.14
r_scbond_it	2.164
r_angle_refined_deg	1.358
r_mcangle_it	1.194
r_mcbond_it	1.003
r_symmetry_hbond_refined	0.409
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.232
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.189
r_chiral_restr	0.098
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4007
Nucleic Acid Atoms
Solvent Atoms	461
Heterogen Atoms	64

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
HKL-2000	data scaling
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.