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Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys F46A 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 2.66 53.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.996 α = 105.801 b = 103.077 β = 105.255 c = 104.801 γ = 92.531
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 2019-05-16 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 1.8 50 97 0.057 9.6 2.4 263527
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 1.8 1.83 0.47 2.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2E2G 1.8 49.252 263395 13337 96.991 0.165 0.1633 0.1779 0.1981 0.2093 RANDOM 24.939
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] 0.097 -1.197 1.123 -1.569 -1.08 1.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.914 r_dihedral_angle_4_deg 19.595 r_dihedral_angle_3_deg 16.859 r_lrange_it 7.248 r_lrange_other 7.192 r_dihedral_angle_1_deg 6.781 r_scangle_it 5.522 r_scangle_other 5.522 r_scbond_it 3.695 r_scbond_other 3.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.914 r_dihedral_angle_4_deg 19.595 r_dihedral_angle_3_deg 16.859 r_lrange_it 7.248 r_lrange_other 7.192 r_dihedral_angle_1_deg 6.781 r_scangle_it 5.522 r_scangle_other 5.522 r_scbond_it 3.695 r_scbond_other 3.695 r_mcangle_it 2.868 r_mcangle_other 2.868 r_mcbond_it 2.087 r_mcbond_other 2.084 r_angle_refined_deg 1.762 r_angle_other_deg 1.451 r_nbd_other 0.285 r_symmetry_xyhbond_nbd_refined 0.239 r_nbd_refined 0.206 r_symmetry_nbd_other 0.192 r_xyhbond_nbd_refined 0.192 r_symmetry_nbd_refined 0.19 r_nbtor_refined 0.172 r_xyhbond_nbd_other 0.145 r_symmetry_xyhbond_nbd_other 0.141 r_symmetry_nbtor_other 0.097 r_chiral_restr 0.092 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 19670 Nucleic Acid Atoms Solvent Atoms 1425 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing