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Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys F80A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 1.0 M Ammonium phosphate monobasic
Crystal Properties Matthews coefficient Solvent content 2.66 53.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.148 α = 106.095 b = 103.156 β = 105.017 c = 105.346 γ = 92.404
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) 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 97.8 0.102 7.5 3.5 168524
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 0.519 2.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2E2G 2.1 49.231 168437 8383 97.703 0.171 0.1685 0.1822 0.2213 0.2292 RANDOM 31.818
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] 0.79 -1.043 1.711 -2.085 -1.498 0.998
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.629 r_dihedral_angle_4_deg 19.915 r_dihedral_angle_3_deg 17.058 r_lrange_it 7.252 r_lrange_other 7.242 r_dihedral_angle_1_deg 6.799 r_scangle_it 5.575 r_scangle_other 5.575 r_scbond_it 3.648 r_scbond_other 3.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.629 r_dihedral_angle_4_deg 19.915 r_dihedral_angle_3_deg 17.058 r_lrange_it 7.252 r_lrange_other 7.242 r_dihedral_angle_1_deg 6.799 r_scangle_it 5.575 r_scangle_other 5.575 r_scbond_it 3.648 r_scbond_other 3.647 r_mcangle_it 3.285 r_mcangle_other 3.285 r_mcbond_it 2.323 r_mcbond_other 2.323 r_angle_refined_deg 1.58 r_angle_other_deg 1.319 r_nbd_other 0.253 r_symmetry_xyhbond_nbd_refined 0.225 r_symmetry_nbd_refined 0.21 r_nbd_refined 0.2 r_symmetry_nbd_other 0.188 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.168 r_symmetry_nbtor_other 0.093 r_symmetry_xyhbond_nbd_other 0.093 r_chiral_restr 0.074 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 19670 Nucleic Acid Atoms Solvent Atoms 941 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing