7A79

Crystal structure of RXR gamma LBD in complexes with palmitic acid and GRIP-1 peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6SJM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1517% PEG 3350, 0.1M potassium citrate
Crystal Properties
Matthews coefficientSolvent content
2.141.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.246α = 90
b = 67.051β = 90
c = 110.7γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0000SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.0546.0199.90.1480.1630.0540.9948.28.530235
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.121000.7820.880.310.75427.9

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 REPLACEMENTTHROUGHOUT6sjm2.0546.0128610157499.840.19790.1950.2483RANDOM39.209
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]
-0.440.71-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.494
r_dihedral_angle_4_deg21.959
r_dihedral_angle_3_deg13.85
r_dihedral_angle_1_deg6.173
r_angle_refined_deg1.351
r_angle_other_deg1.336
r_chiral_restr0.085
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.494
r_dihedral_angle_4_deg21.959
r_dihedral_angle_3_deg13.85
r_dihedral_angle_1_deg6.173
r_angle_refined_deg1.351
r_angle_other_deg1.336
r_chiral_restr0.085
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3612
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms36

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing