3KYT

Crystal structure of orphan nuclear receptor RORgamma in complex with natural ligand


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
1.9938.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.978α = 90
b = 53.978β = 90
c = 162.583γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-FAPS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
12.35500.1222.710.7107362

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.3519.841013851199.910.202390.197490.298RANDOM28.858
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.093
r_dihedral_angle_4_deg20.631
r_dihedral_angle_3_deg20.533
r_dihedral_angle_1_deg7.144
r_scangle_it4.43
r_scbond_it2.917
r_angle_refined_deg1.945
r_mcangle_it1.705
r_mcbond_it1.071
r_symmetry_hbond_refined0.371
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.093
r_dihedral_angle_4_deg20.631
r_dihedral_angle_3_deg20.533
r_dihedral_angle_1_deg7.144
r_scangle_it4.43
r_scbond_it2.917
r_angle_refined_deg1.945
r_mcangle_it1.705
r_mcbond_it1.071
r_symmetry_hbond_refined0.371
r_nbtor_refined0.314
r_nbd_refined0.239
r_symmetry_vdw_refined0.234
r_xyhbond_nbd_refined0.188
r_chiral_restr0.142
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2090
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms29

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling