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Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys 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 2.61 52.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.825 α = 105.878 b = 102.79 β = 105.135 c = 104.435 γ = 92.463
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 97.5 0.06 9.2 3.1 262648
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 0.395 2.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2E2G 1.8 49.432 262196 13261 97.357 0.161 0.1588 0.1937 0.2119 RANDOM 25.348
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] 0.435 -0.706 1.284 -1.488 -1.603 1.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.958 r_dihedral_angle_4_deg 19.91 r_dihedral_angle_3_deg 16.693 r_lrange_it 7.518 r_lrange_other 7.46 r_dihedral_angle_1_deg 6.567 r_scangle_it 5.838 r_scangle_other 5.838 r_scbond_it 3.932 r_scbond_other 3.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.958 r_dihedral_angle_4_deg 19.91 r_dihedral_angle_3_deg 16.693 r_lrange_it 7.518 r_lrange_other 7.46 r_dihedral_angle_1_deg 6.567 r_scangle_it 5.838 r_scangle_other 5.838 r_scbond_it 3.932 r_scbond_other 3.931 r_mcangle_it 2.915 r_mcangle_other 2.915 r_mcbond_it 2.121 r_mcbond_other 2.121 r_angle_refined_deg 1.821 r_angle_other_deg 1.479 r_symmetry_xyhbond_nbd_refined 0.294 r_nbd_other 0.289 r_symmetry_nbd_refined 0.233 r_xyhbond_nbd_refined 0.223 r_nbd_refined 0.211 r_symmetry_nbd_other 0.193 r_symmetry_xyhbond_nbd_other 0.18 r_nbtor_refined 0.174 r_symmetry_nbtor_other 0.099 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19730 Nucleic Acid Atoms Solvent Atoms 1225 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing