6T4W

ROR(gamma)t ligand binding domain in complex with 20-alpha-hydroxycholesterol and allosteric ligand Glenmark


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293none - crystallized in storage buffer upon evaporation
Crystal Properties
Matthews coefficientSolvent content
2.7655.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.317α = 90
b = 108.317β = 90
c = 99.332γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.033218PETRA III, DESYP11

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
11.7154.1699.90.1160.1170.0190.99918.637.337690
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.711.750.731

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 REPLACEMENTTHROUGHOUT6SAL1.7154.1635675192099.840.161670.15960.20003RANDOM33.344
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]
-1.38-0.69-1.384.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.924
r_dihedral_angle_4_deg18.342
r_dihedral_angle_3_deg12.397
r_dihedral_angle_1_deg4.898
r_long_range_B_refined4.269
r_long_range_B_other4.083
r_scangle_other2.91
r_mcangle_it2.682
r_mcangle_other2.681
r_scbond_it2.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.924
r_dihedral_angle_4_deg18.342
r_dihedral_angle_3_deg12.397
r_dihedral_angle_1_deg4.898
r_long_range_B_refined4.269
r_long_range_B_other4.083
r_scangle_other2.91
r_mcangle_it2.682
r_mcangle_other2.681
r_scbond_it2.248
r_scbond_other2.247
r_mcbond_it1.91
r_mcbond_other1.904
r_angle_refined_deg1.15
r_angle_other_deg1.111
r_rigid_bond_restr1.081
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1972
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms69

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing