☰ Navigation Tabs
High resolution structure of selenocysteine containing human GPX4
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 6.5 293 30 % (w/v) PEG 1500, 10 % (v/v) isopropanol, 0.1 M calcium chloride and 0.1 M imidazole/ hydrochloric acid pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.7 27.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.963 α = 90 b = 69 β = 115.12 c = 35.666 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 2M Mirror 2015-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 1.3 34.52 99.6 0.098 8.5 4.7 35608
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 1.3 1.32 91.9 0.569 2 4.1
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 1.3 34.52 33903 1678 99.58 0.12526 0.1238 0.1217 0.15541 0.1543 RANDOM 13.116
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] 0.19 0.53 -0.72 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.271 r_sphericity_free 25.895 r_dihedral_angle_4_deg 17.694 r_dihedral_angle_3_deg 11.868 r_sphericity_bonded 8.448 r_dihedral_angle_1_deg 5.886 r_long_range_B_refined 4.55 r_long_range_B_other 3.708 r_scangle_other 2.505 r_scbond_it 2.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.271 r_sphericity_free 25.895 r_dihedral_angle_4_deg 17.694 r_dihedral_angle_3_deg 11.868 r_sphericity_bonded 8.448 r_dihedral_angle_1_deg 5.886 r_long_range_B_refined 4.55 r_long_range_B_other 3.708 r_scangle_other 2.505 r_scbond_it 2.073 r_scbond_other 2.072 r_rigid_bond_restr 1.641 r_angle_refined_deg 1.573 r_mcangle_other 1.537 r_mcangle_it 1.536 r_angle_other_deg 1.201 r_mcbond_it 1.185 r_mcbond_other 1.153 r_chiral_restr 0.108 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1320 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing