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Crystal structure of Casdatifan bound to HIF2a-B*:ARNT-B* complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.10 M Sodium Acetate, 1.25 M Sodium Fluoride
Crystal Properties Matthews coefficient Solvent content 2.76 55.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.693 α = 90 b = 61.15 β = 90 c = 91.32 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2021-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999858 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.558 45.76 99.6 0.999 13.9 8.1 42717
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.558 1.585 0.695
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.558 45.702 42716 3888 99.546 0.193 0.1914 0.2032 0.214 0.2253 23.743
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] -1.491 2.236 -0.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 31.026 r_dihedral_angle_other_6_deg 15.736 r_dihedral_angle_6_deg 12.245 r_dihedral_angle_3_deg 11.76 r_dihedral_angle_1_deg 7.018 r_lrange_it 4.647 r_lrange_other 4.326 r_dihedral_angle_2_deg 2.084 r_mcangle_it 1.934 r_mcangle_other 1.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 31.026 r_dihedral_angle_other_6_deg 15.736 r_dihedral_angle_6_deg 12.245 r_dihedral_angle_3_deg 11.76 r_dihedral_angle_1_deg 7.018 r_lrange_it 4.647 r_lrange_other 4.326 r_dihedral_angle_2_deg 2.084 r_mcangle_it 1.934 r_mcangle_other 1.934 r_scangle_it 1.894 r_scangle_other 1.894 r_angle_refined_deg 1.167 r_scbond_it 1.103 r_scbond_other 1.101 r_mcbond_it 1.085 r_mcbond_other 1.084 r_angle_other_deg 0.509 r_nbd_refined 0.193 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.167 r_nbd_other 0.146 r_symmetry_nbd_refined 0.127 r_symmetry_xyhbond_nbd_refined 0.075 r_symmetry_nbtor_other 0.073 r_xyhbond_nbd_refined 0.072 r_chiral_restr 0.061 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1772 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PHASER phasing