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Crystal structure of human GPX4 in complex with GXpep-2
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, 0.2M sodium acetate, 25% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.16 42.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.247 α = 90 b = 41.247 β = 90 c = 92.902 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 2016-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1 Photon Factory BL-17A
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 1.2 50 93.4 0.066 25.8 4.7 51699
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 1.2 1.22 55.6 0.135 5.7 2.5
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 (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 1.2 35.72 49112 2558 93.61 0.15087 0.15026 0.1584 0.16249 0.1703 RANDOM 10.569
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 -0.02 -0.05 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.622 r_dihedral_angle_4_deg 17.928 r_dihedral_angle_3_deg 12.101 r_dihedral_angle_1_deg 6.017 r_long_range_B_refined 3.568 r_long_range_B_other 3.313 r_angle_refined_deg 1.639 r_angle_other_deg 1.589 r_scangle_other 1.142 r_mcangle_it 0.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.622 r_dihedral_angle_4_deg 17.928 r_dihedral_angle_3_deg 12.101 r_dihedral_angle_1_deg 6.017 r_long_range_B_refined 3.568 r_long_range_B_other 3.313 r_angle_refined_deg 1.639 r_angle_other_deg 1.589 r_scangle_other 1.142 r_mcangle_it 0.803 r_mcangle_other 0.796 r_scbond_it 0.723 r_scbond_other 0.719 r_mcbond_it 0.465 r_mcbond_other 0.458 r_chiral_restr 0.101 r_bond_other_d 0.011 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 1491 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing