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Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfinic acid form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 0.1M sodium acetate pH4.8, 0.2M calcium chloride, 10%(v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.63 53.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.238 α = 105.88 b = 103.13 β = 105.12 c = 104.683 γ = 92.63
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 2005-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 2.6 50 94.5 80972
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 2.6 2.69 77.5
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 1X0R 2.6 39.37 77674 4086 90.49 0.23374 0.23132 0.2246 0.27961 0.2705 RANDOM 33.813
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] -0.01 -0.02 -0.03 -0.01 -0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.162 r_dihedral_angle_3_deg 15.979 r_dihedral_angle_4_deg 14.783 r_dihedral_angle_1_deg 4.399 r_angle_refined_deg 0.892 r_scangle_it 0.7 r_mcangle_it 0.438 r_scbond_it 0.397 r_nbtor_refined 0.299 r_mcbond_it 0.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.162 r_dihedral_angle_3_deg 15.979 r_dihedral_angle_4_deg 14.783 r_dihedral_angle_1_deg 4.399 r_angle_refined_deg 0.892 r_scangle_it 0.7 r_mcangle_it 0.438 r_scbond_it 0.397 r_nbtor_refined 0.299 r_mcbond_it 0.249 r_nbd_refined 0.164 r_symmetry_vdw_refined 0.146 r_xyhbond_nbd_refined 0.114 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 19328 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing