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Crystal structure of the human RORalpha ligand binding domain in complex with cholesterol sulfate at 2.2A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N83 PDB ENTRY 1N83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.78 55.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.4 α = 90 b = 49.9 β = 97.8 c = 60.7 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH 2002-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9200 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 20 99.7 0.079 0.079 16.2 3.5 16541 16541 32.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 99.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1N83 2.2 20 15671 15671 830 99.57 0.19734 0.19734 0.19672 0.20874 0.2062 RANDOM 35.919
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] 2 -0.79 -0.15 -2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.222 r_scangle_it 4.207 r_dihedral_angle_1_deg 3.301 r_scbond_it 2.509 r_mcangle_it 1.669 r_angle_refined_deg 1.398 r_mcbond_it 0.833 r_angle_other_deg 0.743 r_symmetry_hbond_refined 0.392 r_xyhbond_nbd_other 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.222 r_scangle_it 4.207 r_dihedral_angle_1_deg 3.301 r_scbond_it 2.509 r_mcangle_it 1.669 r_angle_refined_deg 1.398 r_mcbond_it 0.833 r_angle_other_deg 0.743 r_symmetry_hbond_refined 0.392 r_xyhbond_nbd_other 0.323 r_symmetry_vdw_other 0.31 r_nbd_refined 0.255 r_xyhbond_nbd_refined 0.232 r_symmetry_vdw_refined 0.213 r_nbd_other 0.209 r_chiral_restr 0.079 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2066 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DENZO data reduction CCP4 data scaling