☰ Navigation Tabs
Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/F80C/C207S/C213S mutant (ApPrx*F80C)
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 53.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.065 α = 106.026 b = 103.134 β = 104.752 c = 104.956 γ = 92.595
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 16M 2019-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 2.2 50 97.7 0.049 0.997 9 2.3 146036
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 2.2 2.24 0.222 0.927 3.4
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6KRK 2.2 49.227 145744 7443 97.546 0.159 0.1564 0.2072 0.218 44.523
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] 0.006 -0.002 0.004 -0.005 -0.002 -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.58 r_dihedral_angle_4_deg 20.554 r_dihedral_angle_3_deg 18.519 r_lrange_it 8.595 r_lrange_other 8.591 r_scangle_it 6.903 r_scangle_other 6.903 r_dihedral_angle_1_deg 6.876 r_scbond_it 4.707 r_scbond_other 4.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.58 r_dihedral_angle_4_deg 20.554 r_dihedral_angle_3_deg 18.519 r_lrange_it 8.595 r_lrange_other 8.591 r_scangle_it 6.903 r_scangle_other 6.903 r_dihedral_angle_1_deg 6.876 r_scbond_it 4.707 r_scbond_other 4.707 r_mcangle_it 4.499 r_mcangle_other 4.499 r_mcbond_it 3.398 r_mcbond_other 3.397 r_angle_refined_deg 1.616 r_angle_other_deg 1.304 r_nbd_other 0.243 r_symmetry_xyhbond_nbd_refined 0.24 r_nbd_refined 0.203 r_symmetry_nbd_other 0.189 r_symmetry_nbd_refined 0.181 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.168 r_symmetry_nbtor_other 0.092 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.058 r_bond_refined_d 0.009 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 896 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing