2PJL | pdb_00002pjl

Crystal Structure of Human Estrogen-Related Receptor alpha in Complex with a Synthetic Inverse Agonist reveals its Novel Molecular Mechanism

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XB7	PDB ENTRY 1XB7 with H12 removed

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	0.2M MgCl2, 12%PEG400, 0.1M HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.465	α = 90
b = 96.465	β = 90
c = 134.59	γ = 120

Symmetry
Space Group	H 3

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	MAR CCD 165 mm	mirrors	2005-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.8000	SLS	X10SA

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	20	99.5	0.068	0.068	13.5	12.5	20542	20542			48.6

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	99.9		0.242	0.242	4.8	10.4	2055

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 (All)	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 1XB7 with H12 removed	2.3	20	20528	20528	1056	99.4	0.222	0.222	0.219	0.2159	0.281	0.2752	RANDOM	42.43

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]
0.86	0.43		0.86		-1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.015
r_dihedral_angle_4_deg	20.057
r_dihedral_angle_3_deg	16.513
r_dihedral_angle_1_deg	4.433
r_scangle_it	1.685
r_angle_refined_deg	1.127
r_scbond_it	1.062
r_mcangle_it	0.848
r_mcbond_it	0.489
r_nbtor_refined	0.292
r_symmetry_hbond_refined	0.25
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.177
r_xyhbond_nbd_refined	0.175
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3388
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	50

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction