☰ Navigation Tabs
Crystal structure of sulfonic peroxiredoxin Ahp1 in complex with thioredoxin Trx2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 25% polyethylene glycol 3,350, 0.2 M lithium sulfate, 0.1 M HEPES-NaOH, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.5 α = 90 b = 132.8 β = 90 c = 76.99 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2011-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.12 50 100 0.087 0.094 0.035 0.998 14.8 7.1 16850 30.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.23 100 0.493 0.53 0.195 0.904 4.2 7.3
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 4DSS 2.12 38.525 16833 824 99.958 0.213 0.2111 0.2167 0.2439 0.2503 Random selection 33.033
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] -0.552 -0.282 0.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.626 r_dihedral_angle_4_deg 24.755 r_dihedral_angle_3_deg 14.066 r_dihedral_angle_1_deg 6.345 r_lrange_it 5.914 r_lrange_other 5.914 r_scangle_it 4.48 r_scangle_other 4.479 r_mcangle_it 3.93 r_mcangle_other 3.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.626 r_dihedral_angle_4_deg 24.755 r_dihedral_angle_3_deg 14.066 r_dihedral_angle_1_deg 6.345 r_lrange_it 5.914 r_lrange_other 5.914 r_scangle_it 4.48 r_scangle_other 4.479 r_mcangle_it 3.93 r_mcangle_other 3.929 r_scbond_it 2.891 r_scbond_other 2.891 r_mcbond_other 2.666 r_mcbond_it 2.665 r_angle_other_deg 2.316 r_angle_refined_deg 1.413 r_symmetry_xyhbond_nbd_refined 0.522 r_symmetry_nbd_refined 0.269 r_symmetry_nbd_other 0.22 r_nbd_refined 0.204 r_nbd_other 0.186 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.139 r_symmetry_xyhbond_nbd_other 0.075 r_symmetry_nbtor_other 0.07 r_chiral_restr 0.066 r_bond_other_d 0.036 r_gen_planes_other 0.012 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2120 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing