2QA8 | pdb_00002qa8

Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Mutant 537S Complexed with Genistein

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
1.92	35.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.668	α = 90
b = 77.957	β = 109.05
c = 58	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	Rosenbaum-Rock vertical focusing mirror	2004-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97934	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	1.85	50	97	0.049	0.049	20.78	3.1	38560	38560			26.39

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	1.85	1.901	76.29		0.367	0.367	1.79	2.4	2204

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	1.85	19.89	38516	38516	1935	96.85	0.214	0.211	0.21	0.264	0.27	RANDOM	48.196

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]
0.16		-0.01	-0.18		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.498
r_dihedral_angle_4_deg	21.92
r_dihedral_angle_3_deg	17.891
r_scangle_it	11.112
r_scbond_it	8.369
r_mcangle_it	4.979
r_dihedral_angle_1_deg	4.814
r_mcbond_it	3.646
r_angle_refined_deg	1.278
r_nbtor_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.498
r_dihedral_angle_4_deg	21.92
r_dihedral_angle_3_deg	17.891
r_scangle_it	11.112
r_scbond_it	8.369
r_mcangle_it	4.979
r_dihedral_angle_1_deg	4.814
r_mcbond_it	3.646
r_angle_refined_deg	1.278
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.289
r_nbd_refined	0.244
r_xyhbond_nbd_refined	0.208
r_symmetry_hbond_refined	0.194
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3882
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms	40

Software

Software
Software Name	Purpose
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.