7B9O

Crystal structure of Retinoic Acid Receptor alpha (RXRA) in complexed with S169 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MKU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29324% PEG 4000 0.2M Ammonium acetate 0.1M Tris pH7.5
Crystal Properties
Matthews coefficientSolvent content
2.1542.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.529α = 90
b = 65.529β = 90
c = 110.178γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.000SLSX06SA

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
12.0546.3499.20.060.0630.020.99913.1815570
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)
12.052.1199.90.9060.960.3010.8638.2

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 REPLACEMENTTHROUGHOUT5mku2.0546.341475876098.820.19880.19680.2358RANDOM65.286
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]
1.911.91-3.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.26
r_dihedral_angle_4_deg22.969
r_dihedral_angle_3_deg14.418
r_dihedral_angle_1_deg6.356
r_angle_refined_deg1.298
r_angle_other_deg1.277
r_chiral_restr0.078
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.26
r_dihedral_angle_4_deg22.969
r_dihedral_angle_3_deg14.418
r_dihedral_angle_1_deg6.356
r_angle_refined_deg1.298
r_angle_other_deg1.277
r_chiral_restr0.078
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1741
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms30

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing