7XWP | pdb_00007xwp

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GIU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	16-20% PEG3350, 100 mM BisTris pH6.5, 200 mM Magnesium Acetate

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.121	α = 90
b = 89.017	β = 90
c = 101.235	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2019-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.92	46.34	90.1	0.996	8.9	6		33107

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	1.96			0.325	0.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	2giu	1.919	46.383	33061	1639	89.808	0.216	0.2143	0.22	0.2551	0.26	RANDOM	32.643

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]
-0.83			1.171		-0.351

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.208
r_dihedral_angle_4_deg	16.165
r_dihedral_angle_3_deg	14.332
r_dihedral_angle_1_deg	5.822
r_mcangle_it	4.105
r_mcbond_it	2.897
r_mcbond_other	2.893
r_angle_other_deg	2.284
r_angle_refined_deg	1.478
r_chiral_restr	0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.208
r_dihedral_angle_4_deg	16.165
r_dihedral_angle_3_deg	14.332
r_dihedral_angle_1_deg	5.822
r_mcangle_it	4.105
r_mcbond_it	2.897
r_mcbond_other	2.893
r_angle_other_deg	2.284
r_angle_refined_deg	1.478
r_chiral_restr	0.07
r_bond_other_d	0.035
r_gen_planes_other	0.018
r_gen_planes_refined	0.012
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3526
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	76

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	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.