6SJM

Crystal structure of the Retinoic Acid Receptor alpha in complex with compound 24 (JP175)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293.1521% PEG 4000, 0.2 M ammonium acetate and 0.1 M tris, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.0439.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.998α = 90
b = 63.998β = 90
c = 109.596γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-07-06MSINGLE 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
12.5245.2599.20.0710.080.0290.99812.77.38101
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)
12.522.661000.9921.0540.3710.7777.7

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 REPLACEMENTTHROUGHOUT5LYQ2.5245.25767541498.690.20740.20530.247RANDOM80.634
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]
1.351.35-2.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.417
r_dihedral_angle_4_deg18.121
r_dihedral_angle_3_deg15.545
r_dihedral_angle_1_deg6.995
r_angle_refined_deg1.168
r_angle_other_deg1.156
r_chiral_restr0.057
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.417
r_dihedral_angle_4_deg18.121
r_dihedral_angle_3_deg15.545
r_dihedral_angle_1_deg6.995
r_angle_refined_deg1.168
r_angle_other_deg1.156
r_chiral_restr0.057
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1780
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing