2REW

Crystal Structure of PPARalpha ligand binding domain with BMS-631707


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherPreviously determined in house PPARalpha LBD structure

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.7955.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.264α = 90
b = 78.264β = 90
c = 98.715γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152003-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

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
12.355099.70.088.25.728240
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)
2.352.431000.5335.62839

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPreviously determined in house PPARalpha LBD structure2.3530.66150437591000.1990.1970.245RANDOM45.714
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]
0.740.370.74-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.825
r_dihedral_angle_4_deg20.692
r_dihedral_angle_3_deg16.926
r_dihedral_angle_1_deg5.338
r_scangle_it3.148
r_scbond_it2.005
r_mcangle_it1.846
r_angle_refined_deg1.719
r_mcbond_it1.133
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.825
r_dihedral_angle_4_deg20.692
r_dihedral_angle_3_deg16.926
r_dihedral_angle_1_deg5.338
r_scangle_it3.148
r_scbond_it2.005
r_mcangle_it1.846
r_angle_refined_deg1.719
r_mcbond_it1.133
r_nbtor_refined0.306
r_symmetry_vdw_refined0.216
r_nbd_refined0.211
r_xyhbond_nbd_refined0.171
r_chiral_restr0.103
r_symmetry_hbond_refined0.07
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2003
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms63

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling