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Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/K84A/C207S/C213S mutant (ApPrx*K84A)
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, SITTING DROP 293 The reservoir solution contained 0.10 M sodium acetate trihydrate (pH 4.6) 0.20 M calcium chloride dihydrate 20 %v/v 2-propanol.
Crystal Properties Matthews coefficient Solvent content 2.7 54.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.008 α = 90 b = 210.575 β = 90 c = 308.668 γ = 90
Symmetry Space Group P 21 21 21
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 2020-02-08 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 2.9 49.48 99.9 0.162 0.993 8.9 8.3 83831
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 2.9 2.96 100 0.965 0.763 2.2
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 2.9 49.48 83763 4355 99.783 0.183 0.1788 0.1712 0.2559 0.2435 52.418
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] 0.072 -0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.469 r_dihedral_angle_3_deg 21.245 r_dihedral_angle_4_deg 20.907 r_lrange_it 9.81 r_lrange_other 9.81 r_dihedral_angle_1_deg 7.767 r_scangle_it 7.305 r_scangle_other 7.305 r_mcangle_it 6.345 r_mcangle_other 6.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.469 r_dihedral_angle_3_deg 21.245 r_dihedral_angle_4_deg 20.907 r_lrange_it 9.81 r_lrange_other 9.81 r_dihedral_angle_1_deg 7.767 r_scangle_it 7.305 r_scangle_other 7.305 r_mcangle_it 6.345 r_mcangle_other 6.345 r_scbond_it 4.722 r_scbond_other 4.722 r_mcbond_it 4.22 r_mcbond_other 4.22 r_angle_refined_deg 1.656 r_angle_other_deg 1.209 r_symmetry_nbd_refined 0.216 r_nbd_refined 0.209 r_symmetry_xyhbond_nbd_refined 0.209 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.171 r_nbd_other 0.164 r_symmetry_xyhbond_nbd_other 0.14 r_symmetry_nbtor_other 0.094 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23628 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing