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Crystal structure of human glutathione peroxidase 7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GS3 PDB entry 2GS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 25% PEG 3350, 200 mM Ammoniun sulfate, 17% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.95 36.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.046 α = 90 b = 56.224 β = 91.27 c = 94.593 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 CCD MARMOSAIC 225 mm CCD 2007-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.95370 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 32.04 100 0.144 9 3.6 22890 22890 17.8
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 0.575 1.9 3.2 3293
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 PDB entry 2GS3 2 30 21721 21721 1152 99.99 0.166 0.166 0.16338 0.1724 0.2149 0.2204 RANDOM 15.875
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] 0.46 -0.33 -1.79 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.434 r_dihedral_angle_4_deg 17.586 r_dihedral_angle_3_deg 13.62 r_scangle_it 7.25 r_dihedral_angle_1_deg 6.369 r_scbond_it 5.453 r_mcangle_it 3.5 r_mcbond_it 2.812 r_angle_refined_deg 1.432 r_angle_other_deg 0.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.434 r_dihedral_angle_4_deg 17.586 r_dihedral_angle_3_deg 13.62 r_scangle_it 7.25 r_dihedral_angle_1_deg 6.369 r_scbond_it 5.453 r_mcangle_it 3.5 r_mcbond_it 2.812 r_angle_refined_deg 1.432 r_angle_other_deg 0.957 r_mcbond_other 0.795 r_symmetry_vdw_other 0.205 r_nbd_refined 0.196 r_nbd_other 0.189 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.146 r_symmetry_vdw_refined 0.116 r_chiral_restr 0.088 r_nbtor_other 0.086 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 2454 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling PHASER phasing