2GPU

Estrogen Related Receptor-gamma ligand binding domain complexed with 4-hydroxy-tamoxifen


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP828336% Peg600, 0.1M tris, 0.1% zwittergent 3-16, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.7154.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.01α = 90
b = 64.01β = 90
c = 138.23γ = 90
Symmetry
Space GroupP 41 21 2

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
11.750990.0712.93266032333-3-3
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)
1.71.7699.70.3518.5

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 REPLACEMENTTHROUGHOUT2GP71.746.983247332165102599.050.180.180.180.195RANDOM21.881
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]
-0.13-0.130.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.423
r_dihedral_angle_4_deg18.398
r_dihedral_angle_3_deg12.246
r_dihedral_angle_1_deg4.516
r_scangle_it2.794
r_scbond_it2.03
r_angle_refined_deg1.349
r_mcangle_it1.175
r_mcbond_it1.044
r_angle_other_deg0.812
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.423
r_dihedral_angle_4_deg18.398
r_dihedral_angle_3_deg12.246
r_dihedral_angle_1_deg4.516
r_scangle_it2.794
r_scbond_it2.03
r_angle_refined_deg1.349
r_mcangle_it1.175
r_mcbond_it1.044
r_angle_other_deg0.812
r_nbd_refined0.244
r_symmetry_vdw_refined0.233
r_symmetry_hbond_refined0.228
r_symmetry_vdw_other0.198
r_mcbond_other0.185
r_nbtor_refined0.179
r_nbd_other0.168
r_xyhbond_nbd_refined0.135
r_nbtor_other0.085
r_chiral_restr0.067
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1951
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms29

Software

Software
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection