2GPP

Estrogen Related Receptor-gamma ligand binding domain complexed with a RIP140 peptide and synthetic ligand GSK4716


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52959% PEG 20K 0.1M MES buffer, pH 7.5, vapor diffusion, hanging drop, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.6966.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 203.81α = 90
b = 203.81β = 90
c = 53.46γ = 120
Symmetry
Space GroupH 3

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
12.65098.80.0649.52537125066-3-3
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)
2.62.6484.90.4033.2

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 REPLACEMENTTHROUGHOUT2GP72.645.74253722506576498.790.2330.2330.2320.257RANDOM44.602
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]
-0.86-0.43-0.861.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.503
r_dihedral_angle_3_deg15.579
r_dihedral_angle_4_deg14.94
r_dihedral_angle_1_deg5.576
r_scangle_it1.911
r_scbond_it1.222
r_angle_refined_deg1.215
r_mcangle_it0.939
r_angle_other_deg0.733
r_mcbond_it0.609
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.503
r_dihedral_angle_3_deg15.579
r_dihedral_angle_4_deg14.94
r_dihedral_angle_1_deg5.576
r_scangle_it1.911
r_scbond_it1.222
r_angle_refined_deg1.215
r_mcangle_it0.939
r_angle_other_deg0.733
r_mcbond_it0.609
r_nbd_refined0.23
r_symmetry_vdw_other0.198
r_nbtor_refined0.188
r_symmetry_vdw_refined0.178
r_nbd_other0.167
r_xyhbond_nbd_refined0.149
r_mcbond_other0.146
r_nbtor_other0.088
r_chiral_restr0.06
r_bond_refined_d0.011
r_gen_planes_refined0.003
r_symmetry_hbond_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3760
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms21

Software

Software
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection