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Crystal structure of PT3388 bound to HIF2a-B*:ARNT-B* complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XT2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 293 Bis-Tris, pH5.4 and 16% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.253 α = 90 b = 84.006 β = 106.21 c = 41.344 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 315 2015-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97932 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 50 96.4 0.056 0.093 0.049 21.2 3.6 15771
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.09 87.4 0.866 0.565 0.534 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4xt2 2 28.85 14945 804 96.56 0.2145 0.2112 0.2769 0.2611 RANDOM 43.21
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] 2.34 0.24 -0.24 -1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.354 r_dihedral_angle_3_deg 17.625 r_dihedral_angle_4_deg 14.432 r_dihedral_angle_1_deg 7.227 r_angle_refined_deg 2.166 r_chiral_restr 0.123 r_bond_refined_d 0.017 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1732 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing