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Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys W88A 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 293 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 1.0 M Ammonium phosphate monobasic
Crystal Properties Matthews coefficient Solvent content 2.73 54.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.24 α = 105.779 b = 103.285 β = 105.245 c = 105.129 γ = 92.446
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) 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 1.89 50 97.4 0.063 12.3 3.2 230604
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 1.89 1.92 0.465 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 2E2G 1.89 49.368 230599 11796 97.424 0.165 0.1639 0.1788 0.1883 0.1999 28.694
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] 0.223 -0.808 1.136 -1.648 -0.953 1.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.054 r_dihedral_angle_4_deg 21.043 r_dihedral_angle_3_deg 16.61 r_lrange_it 8.148 r_lrange_other 8.116 r_dihedral_angle_1_deg 6.926 r_scangle_it 5.924 r_scangle_other 5.924 r_scbond_it 3.975 r_scbond_other 3.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.054 r_dihedral_angle_4_deg 21.043 r_dihedral_angle_3_deg 16.61 r_lrange_it 8.148 r_lrange_other 8.116 r_dihedral_angle_1_deg 6.926 r_scangle_it 5.924 r_scangle_other 5.924 r_scbond_it 3.975 r_scbond_other 3.972 r_mcangle_it 3.685 r_mcangle_other 3.685 r_mcbond_it 2.628 r_mcbond_other 2.627 r_angle_refined_deg 1.757 r_angle_other_deg 1.392 r_symmetry_xyhbond_nbd_refined 0.407 r_xyhbond_nbd_other 0.316 r_symmetry_nbd_refined 0.278 r_nbd_other 0.249 r_xyhbond_nbd_refined 0.216 r_nbd_refined 0.211 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_other 0.116 r_symmetry_nbtor_other 0.097 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19622 Nucleic Acid Atoms Solvent Atoms 1633 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing