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Human GPX4 in complex with covalent Inhibitor ML162 (S enantiomer)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 Reservoir made from 0.2 M ammonium sulfate, 20% (w/v) PEG 3350. Prio to crystal set-up, the protein was modified with covalent inhibitor, purified via gelfiltration and concentrated to 13.5 mg/ml in 50 mM TrisHCl pH 8.0, 150 mM NaCl, 5mM TCEP
Crystal Properties Matthews coefficient Solvent content 1.87 34.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.734 α = 90 b = 57.249 β = 90 c = 81.311 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 PILATUS 200K 2018-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.54 46.81 86.6 0.1 0.11 0.03 20.2 10.5 20009
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.59 72.1 0.9 0.97 0.33 0.81 2.4 6.7
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.54 46.81 19002 951 86.15 0.15116 0.1495 0.1521 0.18416 0.1853 RANDOM 18.524
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] -0.05 -0.13 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.876 r_dihedral_angle_4_deg 14.775 r_dihedral_angle_3_deg 11.917 r_long_range_B_refined 7.312 r_long_range_B_other 7.143 r_dihedral_angle_1_deg 6.091 r_scangle_other 4.496 r_scbond_it 3.129 r_scbond_other 3.127 r_mcangle_other 2.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.876 r_dihedral_angle_4_deg 14.775 r_dihedral_angle_3_deg 11.917 r_long_range_B_refined 7.312 r_long_range_B_other 7.143 r_dihedral_angle_1_deg 6.091 r_scangle_other 4.496 r_scbond_it 3.129 r_scbond_other 3.127 r_mcangle_other 2.631 r_mcangle_it 2.618 r_angle_refined_deg 1.701 r_mcbond_it 1.667 r_mcbond_other 1.619 r_angle_other_deg 1.023 r_chiral_restr 0.11 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1339 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing