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Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/F80C/C207S/C213S mutant modified with 2-(bromoacetyl)naphthalene(Naph@ApPrx*)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KRK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 The reservoir solution contained 0.10 M sodium citrate (pH5.5) 0.20 M lithium sulfate 15% (v/v) reagent alcohol.
Crystal Properties Matthews coefficient Solvent content 2.65 53.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.999 α = 105.936 b = 103.081 β = 104.945 c = 105.029 γ = 92.381
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 4M 2019-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.1 50 98.1 0.068 0.998 11.8 3.7 169516
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 0.535 0.833 2.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6KRK 2.1 49.244 169364 8444 97.842 0.169 0.1661 0.175 0.2172 0.2215 39.142
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] -0.002 0.004 0.005 0.003 -0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.599 r_dihedral_angle_4_deg 19.593 r_dihedral_angle_3_deg 18.229 r_dihedral_angle_other_3_deg 14.629 r_lrange_it 8.038 r_lrange_other 8.033 r_dihedral_angle_1_deg 6.957 r_scangle_it 6.217 r_scangle_other 6.217 r_scbond_it 4.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.599 r_dihedral_angle_4_deg 19.593 r_dihedral_angle_3_deg 18.229 r_dihedral_angle_other_3_deg 14.629 r_lrange_it 8.038 r_lrange_other 8.033 r_dihedral_angle_1_deg 6.957 r_scangle_it 6.217 r_scangle_other 6.217 r_scbond_it 4.14 r_scbond_other 4.139 r_mcangle_it 3.988 r_mcangle_other 3.987 r_mcbond_it 2.904 r_mcbond_other 2.903 r_angle_other_deg 2.097 r_angle_refined_deg 1.594 r_symmetry_nbd_refined 0.306 r_symmetry_xyhbond_nbd_refined 0.265 r_nbd_other 0.255 r_nbd_refined 0.204 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.153 r_symmetry_xyhbond_nbd_other 0.103 r_symmetry_nbtor_other 0.094 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19680 Nucleic Acid Atoms Solvent Atoms 854 Heterogen Atoms 260
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing