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Peroxiredoxin (wild type) from Aeropyrum pernix K1 (reduced form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M imidazole-HCl, 1M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.78 55.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.609 α = 105.91 b = 104.781 β = 104.92 c = 106.169 γ = 92.88
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 DIP-6040 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.91498 SPring-8 BL44XU
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 2.2 50 94.8 0.095 9.6 2.1 147958
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 2.2 2.28 93.9 0.426 2.3 2 14659
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 2.2 46.83 140122 7414 94.33 0.21198 0.20896 0.209 0.26917 0.2683 RANDOM 31.609
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] 0.04 0.01 0.09 -0.02 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.138 r_dihedral_angle_4_deg 20.528 r_dihedral_angle_3_deg 19.916 r_dihedral_angle_1_deg 7.706 r_scangle_it 5.479 r_scbond_it 3.771 r_angle_refined_deg 2.443 r_mcangle_it 2.293 r_mcbond_it 1.632 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.138 r_dihedral_angle_4_deg 20.528 r_dihedral_angle_3_deg 19.916 r_dihedral_angle_1_deg 7.706 r_scangle_it 5.479 r_scbond_it 3.771 r_angle_refined_deg 2.443 r_mcangle_it 2.293 r_mcbond_it 1.632 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.286 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.188 r_symmetry_hbond_refined 0.175 r_chiral_restr 0.166 r_bond_refined_d 0.033 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 19655 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling