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Crystal structures of a poxviral glutaredoxin in the oxidized and reduced states show redox-correlated structural changes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KTE PDB ENTRY 1KTE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.6 295 0.1 M NaCacodylate pH 5.2, 12.5% MPD, 10 mM Tris pH 8.0, 50 mM NaCl. Cryo solution containing 0.1 M NaCacodylate pH 5.2, 40% MPD and 50 mM GSH added 5 minutes before flash-freezing., pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.13 42.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.627 α = 90 b = 66.668 β = 90 c = 108.096 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC QUANTUM 210 2005-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 54.07 99.6 21297 21297 3.97 1.76
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 1.8 1.87 97.3
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 1KTE 1.8 19.54 21297 21297 1065 99.68 0.18679 0.18679 0.18568 0.1955 0.20804 0.222 RANDOM 28.305
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.986 r_dihedral_angle_4_deg 22.222 r_dihedral_angle_3_deg 16.221 r_scangle_it 8.611 r_dihedral_angle_1_deg 5.971 r_scbond_it 5.96 r_angle_other_deg 3.61 r_mcangle_it 3.311 r_mcbond_it 2.066 r_angle_refined_deg 1.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.986 r_dihedral_angle_4_deg 22.222 r_dihedral_angle_3_deg 16.221 r_scangle_it 8.611 r_dihedral_angle_1_deg 5.971 r_scbond_it 5.96 r_angle_other_deg 3.61 r_mcangle_it 3.311 r_mcbond_it 2.066 r_angle_refined_deg 1.906 r_chiral_restr 0.573 r_symmetry_vdw_other 0.337 r_symmetry_hbond_refined 0.266 r_nbd_other 0.238 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.175 r_symmetry_vdw_refined 0.142 r_nbtor_other 0.107 r_bond_refined_d 0.021 r_gen_planes_other 0.01 r_gen_planes_refined 0.007 r_bond_other_d r_nbtor_refined 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1757 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction CCP4 data scaling XFIT data reduction