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Structure of a mitochondrial type II peroxiredoxin from Pisum sativum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model model generated by EasyPed3D Web Server 1.0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 PEG2000, citrate, NaCl, DTT, 2-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.74 55.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.88 α = 102.94 b = 66.4 β = 104.44 c = 77.23 γ = 99.07
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 BRUKER PLATINUM 200 Microstar micro-focus 2005-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.39 71.9 65.79 0.067 15.416 3.08 30073 30073 22.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.48 0.078
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.8 14.98 27653 25728 2544 93 0.298 0.298 0.277 0.2744 0.292 0.2869 RANDOM 14.29
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] 7.53 -4.01 5.77 -5.66 -0.18 -1.87
RMS Deviations Key Refinement Restraint Deviation x_torsion_deg 23.7 x_scangle_it 2.17 x_angle_deg 1.9 x_mcangle_it 1.65 x_scbond_it 1.41 x_mcbond_it 0.97 x_torsion_impr_deg 0.93 x_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7476 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose SAINT data scaling AMoRE phasing CNS refinement PDB_EXTRACT data extraction PROTEUM PLUS data collection SAINT data reduction XPREP data reduction