2GPV

Estrogen Related Receptor-gamma ligand binding domain complexed with 4-hydroxy-tamoxifen and a SMRT peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GP7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82937% PEG3350 0.2M Lithium Acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1560.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 200.22α = 90
b = 117.17β = 102.36
c = 90.47γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.855090.20.0933.44807943368-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.852.9538.2139.90.2981.4

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 REPLACEMENTTHROUGHOUT2GP72.8519.914759743251135990.870.2210.2210.2190.279RANDOM13.974
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]
1.93-0.550.14-2.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.385
r_dihedral_angle_3_deg17.053
r_dihedral_angle_4_deg14.966
r_dihedral_angle_1_deg5.155
r_scangle_it1.297
r_angle_refined_deg1.164
r_angle_other_deg0.863
r_scbond_it0.83
r_mcangle_it0.536
r_mcbond_it0.335
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.385
r_dihedral_angle_3_deg17.053
r_dihedral_angle_4_deg14.966
r_dihedral_angle_1_deg5.155
r_scangle_it1.297
r_angle_refined_deg1.164
r_angle_other_deg0.863
r_scbond_it0.83
r_mcangle_it0.536
r_mcbond_it0.335
r_symmetry_vdw_other0.252
r_nbd_refined0.231
r_nbtor_refined0.183
r_nbd_other0.18
r_symmetry_vdw_refined0.17
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.147
r_nbtor_other0.086
r_mcbond_other0.068
r_chiral_restr0.056
r_xyhbond_nbd_other0.027
r_bond_refined_d0.01
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10545
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms174

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
PHENIXphasing