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HIF prolyl hydroxylase 2 in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JZR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M Ammonium phosphate monobasic, 0.1M Tris (8.3 8.7),
40% MPD
Crystal Properties Matthews coefficient Solvent content 2.26 45.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.415 α = 90 b = 82.415 β = 90 c = 63.472 γ = 120
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 PILATUS3 6M 2024-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9785 SSRF BL18U1
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 2.5 47.43 99.9 0.98 9.2 7.2 8584
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 2.5 2.6 0.699
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 2.5 47.43 8578 410 99.825 0.228 0.2255 0.228 0.2907 0.2975 70
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] 0.977 0.488 0.977 -3.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.59 r_dihedral_angle_3_deg 10.195 r_dihedral_angle_1_deg 6.183 r_lrange_it 5.612 r_lrange_other 5.572 r_dihedral_angle_2_deg 4.2 r_mcangle_it 3.678 r_mcangle_other 3.676 r_scangle_it 3.448 r_scangle_other 3.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.59 r_dihedral_angle_3_deg 10.195 r_dihedral_angle_1_deg 6.183 r_lrange_it 5.612 r_lrange_other 5.572 r_dihedral_angle_2_deg 4.2 r_mcangle_it 3.678 r_mcangle_other 3.676 r_scangle_it 3.448 r_scangle_other 3.446 r_mcbond_other 2.218 r_mcbond_it 2.217 r_scbond_it 2.085 r_scbond_other 2.062 r_angle_refined_deg 0.744 r_angle_other_deg 0.269 r_nbd_other 0.204 r_nbd_refined 0.197 r_nbtor_refined 0.178 r_symmetry_nbd_other 0.177 r_symmetry_nbd_refined 0.167 r_xyhbond_nbd_refined 0.128 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.035 r_chiral_restr_other 0.022 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1558 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing