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Structure of PHD2 in complex with HIF2a-CODD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L9B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 32.5% (w/v) PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 1.7 27.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.078 α = 90 b = 37.597 β = 90 c = 42.148 γ = 90
Symmetry Space Group P 21 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 EIGER X 16M 2021-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97933 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.8 129.08 100 0.117 0.126 0.047 0.998 8.4 7.1 19834 20.58
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 1.8 1.83 100 0.79 0.86 0.334 0.695 0.8 6.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5L9B 1.8 42.183 19760 946 99.838 0.175 0.173 0.173 0.2134 0.2128 Random 29.036
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] -0.715 -0.482 1.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.087 r_dihedral_angle_3_deg 15.24 r_dihedral_angle_4_deg 14.35 r_dihedral_angle_1_deg 7.198 r_lrange_it 6.248 r_lrange_other 6.23 r_scangle_it 4.837 r_scangle_other 4.835 r_mcangle_it 3.078 r_mcangle_other 3.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.087 r_dihedral_angle_3_deg 15.24 r_dihedral_angle_4_deg 14.35 r_dihedral_angle_1_deg 7.198 r_lrange_it 6.248 r_lrange_other 6.23 r_scangle_it 4.837 r_scangle_other 4.835 r_mcangle_it 3.078 r_mcangle_other 3.076 r_scbond_it 3.023 r_scbond_other 3.022 r_mcbond_it 2.037 r_mcbond_other 2.037 r_angle_refined_deg 1.368 r_angle_other_deg 0.461 r_symmetry_nbd_refined 0.272 r_nbd_refined 0.235 r_nbd_other 0.223 r_symmetry_xyhbond_nbd_refined 0.215 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.142 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.066 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1888 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing