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Crystal structure of Bovine Mitochondrial Peroxiredoxin III
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZYE PDB ENTRY 1ZYE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.1 289 containing 36% 2-Methyl-1,3-Propanediol, 0.1M phosphate-citrate, pH 4.1, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.89 57.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.895 α = 90 b = 290.885 β = 90 c = 81.139 γ = 90
Symmetry Space Group P 21 21 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 315r 2008-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 2.4 288.67 97.7 0.073 11.3 4.1 133014 130007
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 2.4 2.53 93.9 0.732 1.8 3.5
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 (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 1ZYE 2.4 102.14 126310 123547 6556 97.88 0.184 0.18202 0.182 0.22116 0.2205 RANDOM 54.325
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] 0.51 -2.45 1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.043 r_dihedral_angle_4_deg 19.122 r_dihedral_angle_3_deg 17.395 r_dihedral_angle_1_deg 6.411 r_mcangle_it 3.962 r_scbond_it 3.202 r_mcbond_it 2.5 r_angle_refined_deg 1.581 r_chiral_restr 0.108 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.043 r_dihedral_angle_4_deg 19.122 r_dihedral_angle_3_deg 17.395 r_dihedral_angle_1_deg 6.411 r_mcangle_it 3.962 r_scbond_it 3.202 r_mcbond_it 2.5 r_angle_refined_deg 1.581 r_chiral_restr 0.108 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15631 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 49
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling