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Crystal structure of human nuclear receptor sf-1 (nr5a1) bound to its hormone pip3 at 2.4 a resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YOW PDB entry 1YOW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 10% PEG 8K, 0.025M MGOAC, 30% GLYCEROL, 0.067MM PIP3, 0.80MM 14MER EEPSLLKKLLLAPA, NANODROP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
Crystal Properties Matthews coefficient Solvent content 3.32 62.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.85 α = 90 b = 74.85 β = 90 c = 139.63 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 PIXEL DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2013-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 29.165 99.6 0.043 24.6 11.9 16205 16205
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 98.5 0.71 0.71 1.1 8.9 1136
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 1YOW 2.4 29.165 2.03 16099 803 99.52 0.1914 0.1895 0.1925 0.2296 0.2346 76.3499
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 f_dihedral_angle_d 20.036 f_angle_d 0.589 f_chiral_restr 0.04 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2038 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 75
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction PHENIX refinement SCALA data scaling MOSFLM data reduction PHASER phasing