☰ Navigation Tabs
Crystal structure of the selenocysteine to cysteine mutant of human glutathionine peroxidase 2 (GPX2)
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 7.5 293 20% PEG 3350, 200 mM sodium formate, 100 mM Bis-Tris propane, 10% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.01 59.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.308 α = 90 b = 117.212 β = 90 c = 120.157 γ = 90
Symmetry Space Group I 2 2 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 2006-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9183 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 2.1 42 99.8 0.137 14.9 9.1 17619 17619 27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 98.7 3.2 6.3 2496
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 2.1 42 16588 16588 890 99.73 0.15833 0.15833 0.15583 0.1646 0.20481 0.208 RANDOM 21.278
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] 1.44 -0.91 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.269 r_dihedral_angle_3_deg 12.29 r_dihedral_angle_4_deg 10.771 r_scangle_it 8.134 r_dihedral_angle_1_deg 6.564 r_scbond_it 6.059 r_mcangle_it 3.746 r_mcbond_it 2.74 r_angle_refined_deg 1.464 r_angle_other_deg 0.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.269 r_dihedral_angle_3_deg 12.29 r_dihedral_angle_4_deg 10.771 r_scangle_it 8.134 r_dihedral_angle_1_deg 6.564 r_scbond_it 6.059 r_mcangle_it 3.746 r_mcbond_it 2.74 r_angle_refined_deg 1.464 r_angle_other_deg 0.958 r_mcbond_other 0.712 r_symmetry_vdw_other 0.312 r_nbd_refined 0.199 r_nbd_other 0.197 r_nbtor_refined 0.182 r_symmetry_hbond_refined 0.146 r_symmetry_vdw_refined 0.142 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.087 r_nbtor_other 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 1504 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PHASER phasing