7Y8F | pdb_00007y8f

Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with an Inhibitor 30o and GRIP Peptide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DI7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295.15	18% (w/v) PEG 3350, 0.25 M Ammonium sulfate, and 0.1 M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.741	α = 90
b = 101.584	β = 90
c = 195.304	γ = 90

Symmetry
Space Group	C 2 2 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	CMOS	BRUKER PHOTON 100		2021-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	BRUKER METALJET	1.34138

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.22	35.22	99.9	0.0771	13.23	8.4		26472

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.22	2.25	99.4		0.4425	2.25

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	5DI7	2.22	35.22	25034	1322	99.73	0.1913	0.1882	0.2	0.2514	0.26	RANDOM	45.948

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]
-0.45			2.79		-2.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.393
r_dihedral_angle_4_deg	22.231
r_dihedral_angle_3_deg	17.211
r_dihedral_angle_1_deg	6.759
r_angle_refined_deg	1.779
r_angle_other_deg	1.365
r_chiral_restr	0.176
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.393
r_dihedral_angle_4_deg	22.231
r_dihedral_angle_3_deg	17.211
r_dihedral_angle_1_deg	6.759
r_angle_refined_deg	1.779
r_angle_other_deg	1.365
r_chiral_restr	0.176
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3746
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement
SADABS	data scaling
PDB_EXTRACT	data extraction
SAINT	data reduction
PHASER	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.