2QXS | pdb_00002qxs

Crystal Structure of Antagonizing Mutant 536S of the Estrogen Receptor Alpha Ligand Binding Domain Complexed to Raloxifene

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ERR	PDB entry 1err

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.588	α = 90
b = 58.102	β = 102.66
c = 87.95	γ = 90

Symmetry
Space Group	C 1 2 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	MARMOSAIC 300 mm CCD	Rosenbaum-Rock vertical focusing mirror	2006-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.9764	APS	22-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	1.7	20	99.9	0.066	0.066	22.3	6.7	55230	55230			18.7

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)
	1.7	1.76	99		0.303	0.303	5.5	4.5	5450

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 1err	1.7	15	55018	55018	2795	99.85	0.184	0.183	0.22	0.216	0.24	RANDOM	10.195

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]
-0.07		-0.04	0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.012
r_dihedral_angle_4_deg	19.098
r_dihedral_angle_3_deg	15.045
r_dihedral_angle_1_deg	8.38
r_scangle_it	3.048
r_scbond_it	2.072
r_angle_refined_deg	1.464
r_mcangle_it	1.163
r_mcbond_it	0.788
r_symmetry_hbond_refined	0.377

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.012
r_dihedral_angle_4_deg	19.098
r_dihedral_angle_3_deg	15.045
r_dihedral_angle_1_deg	8.38
r_scangle_it	3.048
r_scbond_it	2.072
r_angle_refined_deg	1.464
r_mcangle_it	1.163
r_mcbond_it	0.788
r_symmetry_hbond_refined	0.377
r_xyhbond_nbd_refined	0.359
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.261
r_nbd_refined	0.233
r_chiral_restr	0.178
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3645
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms	68

Software

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

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.