1XB7

X-ray structure of ERRalpha LBD in complex with a PGC-1alpha peptide at 2.5A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KV6PDB ENTRY 1KV6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277NaCl, KI, PEG4000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.362

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.999α = 90
b = 109.999β = 90
c = 104.671γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.8000SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.52094.70.09927.512.3127041270450.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.52.5991.50.412.81186

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 1KV62.520120601206062594.80.21650.21650.214910.2473RANDOM38.271
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]
-0.59-0.3-0.590.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.355
r_scangle_it3.798
r_scbond_it2.104
r_mcangle_it1.599
r_angle_refined_deg1.447
r_angle_other_deg0.953
r_mcbond_it0.83
r_symmetry_hbond_refined0.339
r_symmetry_vdw_other0.28
r_nbd_other0.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.355
r_scangle_it3.798
r_scbond_it2.104
r_mcangle_it1.599
r_angle_refined_deg1.447
r_angle_other_deg0.953
r_mcbond_it0.83
r_symmetry_hbond_refined0.339
r_symmetry_vdw_other0.28
r_nbd_other0.222
r_nbd_refined0.214
r_xyhbond_nbd_refined0.168
r_symmetry_vdw_refined0.167
r_nbtor_other0.081
r_chiral_restr0.076
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1741
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing