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Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/F80C/C207S/C213S mutant modified with 2-bromoacetophenone(Ph@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 53.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.035 α = 106.002 b = 102.986 β = 104.756 c = 105.169 γ = 92.548
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 PILATUS 6M 2019-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0 SPring-8 BL45XU
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 98.3 0.08 0.996 10.1 3.6 168919
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 0.391 0.889 3
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 49.168 168916 8400 98.328 0.162 0.1591 0.1695 0.2101 0.2143 33.297
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] -0.011 0.002 0.001 0.008 0.006 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.509 r_dihedral_angle_4_deg 19.457 r_dihedral_angle_3_deg 17.945 r_lrange_it 7.912 r_lrange_other 7.897 r_dihedral_angle_1_deg 6.854 r_scangle_it 6.027 r_scangle_other 6.026 r_scbond_it 3.929 r_scbond_other 3.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.509 r_dihedral_angle_4_deg 19.457 r_dihedral_angle_3_deg 17.945 r_lrange_it 7.912 r_lrange_other 7.897 r_dihedral_angle_1_deg 6.854 r_scangle_it 6.027 r_scangle_other 6.026 r_scbond_it 3.929 r_scbond_other 3.929 r_mcangle_it 3.665 r_mcangle_other 3.664 r_mcbond_it 2.596 r_mcbond_other 2.594 r_angle_refined_deg 1.666 r_angle_other_deg 1.342 r_nbd_other 0.262 r_nbd_refined 0.203 r_symmetry_xyhbond_nbd_refined 0.199 r_symmetry_nbd_other 0.193 r_symmetry_nbd_refined 0.193 r_symmetry_xyhbond_nbd_other 0.182 r_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.172 r_symmetry_nbtor_other 0.094 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 1146 Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing