2PJL

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XB7PDB ENTRY 1XB7 with H12 removed

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52770.2M MgCl2, 12%PEG400, 0.1M HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2344.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.465α = 90
b = 96.465β = 90
c = 134.59γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2005-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.8000SLSX10SA

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.32099.50.0680.06813.512.5205422054248.6
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)RedundancyNumber Unique Reflections (All)
12.32.3899.90.2420.2424.810.42055

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1XB7 with H12 removed2.3202052820528105699.40.2220.2220.2190.281RANDOM42.43
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]
0.860.430.86-1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.015
r_dihedral_angle_4_deg20.057
r_dihedral_angle_3_deg16.513
r_dihedral_angle_1_deg4.433
r_scangle_it1.685
r_angle_refined_deg1.127
r_scbond_it1.062
r_mcangle_it0.848
r_mcbond_it0.489
r_nbtor_refined0.292
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.015
r_dihedral_angle_4_deg20.057
r_dihedral_angle_3_deg16.513
r_dihedral_angle_1_deg4.433
r_scangle_it1.685
r_angle_refined_deg1.127
r_scbond_it1.062
r_mcangle_it0.848
r_mcbond_it0.489
r_nbtor_refined0.292
r_symmetry_hbond_refined0.25
r_nbd_refined0.195
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.175
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3388
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms50

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction