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Crystal structure of human glutathione peroxidase 3 (selenocysteine to glycine mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I3Y PDB entry 2I3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 0.1M PCB pH 8.0, 60% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.39 63.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.72 α = 90 b = 61.308 β = 90 c = 100.4 γ = 90
Symmetry Space Group P 21 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 2007-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00721 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.85 38.84 99.9 0.086 0.099 12.5 4.1 226425 226199 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.95 100 0.664 0.763 2.3 4.1 7975
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 (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 PDB entry 2I3Y 1.85 38 55398 52544 2807 99.91 0.15269 0.1511 0.1612 0.18263 0.1904 RANDOM 21.621
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] 0.75 -0.27 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.123 r_dihedral_angle_4_deg 16.304 r_dihedral_angle_3_deg 12.516 r_scangle_it 8.75 r_scbond_it 6.272 r_dihedral_angle_1_deg 6.239 r_mcangle_it 3.834 r_mcbond_it 2.52 r_angle_refined_deg 1.414 r_angle_other_deg 1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.123 r_dihedral_angle_4_deg 16.304 r_dihedral_angle_3_deg 12.516 r_scangle_it 8.75 r_scbond_it 6.272 r_dihedral_angle_1_deg 6.239 r_mcangle_it 3.834 r_mcbond_it 2.52 r_angle_refined_deg 1.414 r_angle_other_deg 1.2 r_mcbond_other 0.846 r_symmetry_vdw_other 0.256 r_nbd_refined 0.21 r_nbd_other 0.187 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.151 r_metal_ion_refined 0.094 r_symmetry_vdw_refined 0.093 r_chiral_restr 0.092 r_nbtor_other 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 3013 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling PHASER phasing