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Structure of Human Peroxiredoxin 3 as three stacked rings
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZYE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 12.5% PEG1000, 12.5% PEG3350. 12.5% MPD, 0.02 M alcohol additives at pH 8.5 (Gorrec, 2009)
Crystal Properties Matthews coefficient Solvent content 3.21 61.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.188 α = 90 b = 168.73 β = 90 c = 221.55 γ = 90
Symmetry Space Group I 2 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 ADSC QUANTUM 315 2015-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.979 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.8 52.27 99.8 0.176 0.954 6.6 12.7 61455
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 2.8 2.87 99.7 0.713 12.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1ZYE 2.8 52.27 58445 3005 99.7 0.1849 0.1826 0.189 0.2288 0.2292 RANDOM 22.738
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] -1.15 1.8 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.219 r_dihedral_angle_4_deg 15.771 r_dihedral_angle_3_deg 15.124 r_dihedral_angle_1_deg 6.389 r_mcangle_it 1.587 r_angle_refined_deg 1.378 r_angle_other_deg 0.939 r_mcbond_it 0.897 r_mcbond_other 0.897 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.219 r_dihedral_angle_4_deg 15.771 r_dihedral_angle_3_deg 15.124 r_dihedral_angle_1_deg 6.389 r_mcangle_it 1.587 r_angle_refined_deg 1.378 r_angle_other_deg 0.939 r_mcbond_it 0.897 r_mcbond_other 0.897 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13658 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing