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Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F3L PDB entries 4F3L, 3F1P, & 4M4X experimental model PDB 3F1P PDB entries 4F3L, 3F1P, & 4M4X experimental model PDB 4M4X PDB entries 4F3L, 3F1P, & 4M4X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 2% Tacsimate, pH 7.0, 6% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.09 41.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.006 α = 90.06 b = 76.463 β = 90.19 c = 98.817 γ = 73.13
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 2015-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.35 50 98.4 0.061 0.077 0.046 13 2.6 55780
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 97.4 0.7 0.9 0.557 0.555 2.5 2751
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 FREE R-VALUE PDB entries 4F3L, 3F1P, & 4M4X 2.355 49.408 1.96 55769 2880 98.2 0.2032 0.2001 0.2066 0.232 0.2272 63.9473
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 14.845 f_angle_d 1.403 f_chiral_restr 0.06 f_bond_d 0.011 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8924 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 data scaling Coot model building PHENIX refinement PDB_EXTRACT data extraction PHASER phasing HKL-3000 data reduction