☰ Navigation Tabs
Crystal structure of the selenocysteine to glycine mutant of human glutathione peroxidase 4(GPX4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F8A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 293 20% PEG 3350, 0.2 M ammonium chloride, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.58 73.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.945 α = 90 b = 62.945 β = 90 c = 195.984 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2006-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.95 SLS X10SA
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 1.9 50 99.9 0.096 12.9 5.7 32109 32109 33.4
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 1.9 2 100 0.415 3.5 4.7 4550
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2F8A 1.9 50 30562 30562 1487 99.88 0.17251 0.17251 0.17163 0.1785 0.1908 0.201 RANDOM 33.285
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] 0.99 0.99 -1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.715 r_dihedral_angle_4_deg 20.769 r_dihedral_angle_3_deg 13.003 r_scangle_it 8.532 r_scbond_it 6.76 r_dihedral_angle_1_deg 6.024 r_mcangle_it 4.394 r_mcbond_it 3.123 r_angle_refined_deg 1.361 r_angle_other_deg 0.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.715 r_dihedral_angle_4_deg 20.769 r_dihedral_angle_3_deg 13.003 r_scangle_it 8.532 r_scbond_it 6.76 r_dihedral_angle_1_deg 6.024 r_mcangle_it 4.394 r_mcbond_it 3.123 r_angle_refined_deg 1.361 r_angle_other_deg 0.891 r_mcbond_other 0.888 r_nbd_refined 0.216 r_symmetry_vdw_other 0.196 r_nbd_other 0.19 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.149 r_symmetry_vdw_refined 0.144 r_symmetry_hbond_refined 0.11 r_chiral_restr 0.086 r_nbtor_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1361 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing