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Crystal structure of RORgamma in complex with novel inverse agonist
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.29 49.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.644 α = 90 b = 61.644 β = 90 c = 155.618 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2021-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97918 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.18 57.31 98.73 0.124 16.3 12 15513
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.231 0.348
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.18 48.36 15513 819 98.73 0.20436 0.20193 0.2091 0.25093 0.2533 RANDOM 32.167
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.017 r_dihedral_angle_4_deg 23.572 r_dihedral_angle_3_deg 19.983 r_long_range_B_refined 7.914 r_long_range_B_other 7.913 r_scangle_other 6.315 r_dihedral_angle_1_deg 5.873 r_scbond_it 4.036 r_scbond_other 4.034 r_mcangle_other 3.781
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.017 r_dihedral_angle_4_deg 23.572 r_dihedral_angle_3_deg 19.983 r_long_range_B_refined 7.914 r_long_range_B_other 7.913 r_scangle_other 6.315 r_dihedral_angle_1_deg 5.873 r_scbond_it 4.036 r_scbond_other 4.034 r_mcangle_other 3.781 r_mcangle_it 3.778 r_mcbond_it 2.655 r_mcbond_other 2.654 r_angle_refined_deg 1.711 r_angle_other_deg 0.556 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2067 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing