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Crystal structure of human glutathione peroxidase 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F8A pdb entry 2F8A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 20% PEG 3350, 0.2 M sodium formate, 5% ETHYLENE GLYCOL, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.544 α = 90 b = 104.544 β = 90 c = 71.663 γ = 120
Symmetry Space Group P 62 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 2006-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.8983 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 50 99.9 0.064 23 10.6 16114 16114 27
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 2 2.11 100 0.417 5.7 10.7 2305
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 2F8A 2 50 15269 15269 822 99.81 0.17718 0.17466 0.1808 0.22835 0.2283 RANDOM 37.321
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] -2.7 -1.35 -2.7 4.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.763 r_dihedral_angle_3_deg 14.499 r_dihedral_angle_4_deg 8.149 r_dihedral_angle_1_deg 7.087 r_scangle_it 6.61 r_scbond_it 5.325 r_mcangle_it 3.558 r_mcbond_it 2.832 r_angle_refined_deg 1.458 r_angle_other_deg 0.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.763 r_dihedral_angle_3_deg 14.499 r_dihedral_angle_4_deg 8.149 r_dihedral_angle_1_deg 7.087 r_scangle_it 6.61 r_scbond_it 5.325 r_mcangle_it 3.558 r_mcbond_it 2.832 r_angle_refined_deg 1.458 r_angle_other_deg 0.923 r_mcbond_other 0.786 r_symmetry_vdw_other 0.319 r_nbd_other 0.197 r_nbd_refined 0.192 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.161 r_symmetry_vdw_refined 0.157 r_nbtor_other 0.09 r_chiral_restr 0.088 r_bond_refined_d 0.015 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_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 1474 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling PHASER phasing