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Crystal structure of the selenocysteine to glycine mutant of human glutathione peroxidase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GP1 PDB ENTRY 1GP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 35% TACSIMATE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.89 57.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.592 α = 90 b = 59.376 β = 119.41 c = 81.132 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARRESEARCH 2005-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9791 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 1.5 70.71 95.7 0.54 15.4 3.5 80997 80997 13
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 1.5 1.58 75.2 0.306 2.9 2.5 9180
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 1GP1 1.5 70.71 79080 79080 1917 95.71 0.138 0.13803 0.13758 0.1388 0.15636 0.1395 RANDOM 15.233
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] -0.71 -0.15 0.87 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.446 r_dihedral_angle_4_deg 17.589 r_dihedral_angle_3_deg 11.174 r_scangle_it 5.887 r_dihedral_angle_1_deg 5.823 r_scbond_it 3.965 r_mcangle_it 2.692 r_mcbond_it 2.028 r_angle_refined_deg 1.414 r_angle_other_deg 0.913
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.446 r_dihedral_angle_4_deg 17.589 r_dihedral_angle_3_deg 11.174 r_scangle_it 5.887 r_dihedral_angle_1_deg 5.823 r_scbond_it 3.965 r_mcangle_it 2.692 r_mcbond_it 2.028 r_angle_refined_deg 1.414 r_angle_other_deg 0.913 r_mcbond_other 0.499 r_symmetry_vdw_other 0.274 r_nbd_refined 0.217 r_nbd_other 0.206 r_nbtor_refined 0.181 r_symmetry_vdw_refined 0.162 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.086 r_nbtor_other 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 2860 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing