5LWP

Discovery of phenoxyindazoles and phenylthioindazoles as RORg inverse agonists


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3B0W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2780.1M Hepes pH8.5, 0.1M MgCl2, 7% PEG6000
Crystal Properties
Matthews coefficientSolvent content
3.4964.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 173.81α = 90
b = 173.81β = 90
c = 68.4γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray278PIXELDECTRIS PILATUS 6MKirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal2014-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.97857SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.429.31399.70.0570.99921.987.0715503-355.298
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5499.10.5090.9233.987.1

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 REPLACEMENTTHROUGHOUT3B0W2.429.311472677699.750.20280.20010.2533RANDOM52.239
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]
-1.16-0.58-1.163.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.146
r_dihedral_angle_4_deg19.915
r_dihedral_angle_3_deg18.366
r_scbond_it6.716
r_mcangle_it6.528
r_dihedral_angle_1_deg6.168
r_mcbond_it4.736
r_angle_refined_deg1.992
r_chiral_restr0.139
r_bond_refined_d0.018
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.146
r_dihedral_angle_4_deg19.915
r_dihedral_angle_3_deg18.366
r_scbond_it6.716
r_mcangle_it6.528
r_dihedral_angle_1_deg6.168
r_mcbond_it4.736
r_angle_refined_deg1.992
r_chiral_restr0.139
r_bond_refined_d0.018
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1984
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms35

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction