2QXM | pdb_00002qxm

Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed to Burned Meat Compound PhIP

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		8.5	298	0.2M Magnesium chloride hexahydrate, 0.1M Tris 8.5, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.50

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.965	α = 90
b = 83.703	β = 108.7
c = 58.427	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	MARMOSAIC 325 mm CCD	FLAT MIRROR (VERTICAL FOCUSING)	2007-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	2.3	12	88.8	0.12	0.12	16.7	3.3		20199			46.85

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	2.3	2.38	86.9		0.241	0.241	3.73	3

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	2.3	11.96	20138	20138	1040	88.5	0.274	0.273	0.27	0.296	0.3	RANDOM	26.26

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]
-0.26		-0.34	-0.45		0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.002
r_dihedral_angle_4_deg	23.685
r_dihedral_angle_3_deg	18.729
r_scangle_it	15.056
r_scbond_it	14.837
r_mcangle_it	11.031
r_mcbond_it	10.175
r_dihedral_angle_1_deg	6.294
r_angle_other_deg	2.739
r_angle_refined_deg	1.54
r_mcbond_other	1.367
r_symmetry_hbond_refined	1.098
r_symmetry_vdw_other	0.401
r_symmetry_vdw_refined	0.268
r_nbd_other	0.256
r_nbd_refined	0.24
r_nbtor_refined	0.195
r_xyhbond_nbd_refined	0.149
r_nbtor_other	0.1
r_chiral_restr	0.093
r_xyhbond_nbd_other	0.048
r_bond_refined_d	0.018
r_bond_other_d	0.01
r_gen_planes_other	0.009
r_gen_planes_refined	0.006
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3927
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	34

Software

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