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Peroxiredoxin from Pyrococcus horikoshii (6m mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.1 M sodium acetate (pH 5.0), 0.2 M magnesium chloride, and 19% PEG400
Crystal Properties Matthews coefficient Solvent content 2.73 54.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.583 α = 90 b = 98.598 β = 119.95 c = 137.571 γ = 90
Symmetry Space Group P 1 21 1
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 RAYONIX MX-225 2016-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1 SPring-8 BL38B1
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 2.25 40 98.9 6.4 3.3 150002
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3W6G 2.25 39.73 143844 7632 99.67 0.19533 0.19336 0.23191 0.2208 RANDOM 33.374
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 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.018 r_dihedral_angle_3_deg 20.613 r_dihedral_angle_4_deg 16.36 r_dihedral_angle_1_deg 8.167 r_angle_refined_deg 2.161 r_angle_other_deg 1.001 r_chiral_restr 0.15 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.018 r_dihedral_angle_3_deg 20.613 r_dihedral_angle_4_deg 16.36 r_dihedral_angle_1_deg 8.167 r_angle_refined_deg 2.161 r_angle_other_deg 1.001 r_chiral_restr 0.15 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it 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 20700 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing