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Crystal structure of human GPX4 in complex with GXpep-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OBI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1M Tris pH 8.5, 0.1M potassium formate, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.1 41.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.746 α = 90 b = 72.242 β = 108.41 c = 39.616 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS3 6M 2016-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.1 50 99.8 0.044 13.3 3.4 65137
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.12 81.4 0.572 2.2 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2OBI 1.1 37.59 61861 3245 91.99 0.1644 0.16341 0.1729 0.18368 0.1911 RANDOM 13.236
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] -0.33 0.31 -0.18 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.018 r_dihedral_angle_4_deg 17.481 r_dihedral_angle_3_deg 12.531 r_dihedral_angle_1_deg 5.722 r_long_range_B_refined 3.683 r_long_range_B_other 3.526 r_angle_refined_deg 1.576 r_scangle_other 1.438 r_mcangle_it 1.022 r_mcangle_other 1.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.018 r_dihedral_angle_4_deg 17.481 r_dihedral_angle_3_deg 12.531 r_dihedral_angle_1_deg 5.722 r_long_range_B_refined 3.683 r_long_range_B_other 3.526 r_angle_refined_deg 1.576 r_scangle_other 1.438 r_mcangle_it 1.022 r_mcangle_other 1.022 r_angle_other_deg 1.018 r_scbond_it 0.887 r_scbond_other 0.886 r_mcbond_it 0.61 r_mcbond_other 0.61 r_chiral_restr 0.353 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 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 1462 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing