☰ Navigation Tabs
Crystal structure of an atypical two-cysteine peroxiredoxin (SAOUHSC_01822) from Staphylococcus aureus NCTC8325
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PSQ PDB ENTRY 1PSQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 2.0M AMMONIUM SULPHATE, 0.1M NA-HEPES PH 7, 2% (V/V) PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.19 61.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.5 α = 90 b = 149.356 β = 104.43 c = 73.736 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ Mirrors 2009-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.956 74.678 92.9 0.047 14.7 3.3 60849 60849
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.06 71.5 0.341 0.341 0.465 0.273 2.3 2.5 6820
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PSQ 1.96 19.85 60800 3072 92.71 0.1702 0.1683 0.2057 0.191 RANDOM 29.418
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] 1.71 0.55 -1.07 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.91 r_dihedral_angle_4_deg 15.735 r_dihedral_angle_3_deg 15.52 r_dihedral_angle_1_deg 7.078 r_scangle_it 4.85 r_scbond_it 3.106 r_angle_refined_deg 1.932 r_mcangle_it 1.785 r_mcbond_it 1.095 r_chiral_restr 0.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.91 r_dihedral_angle_4_deg 15.735 r_dihedral_angle_3_deg 15.52 r_dihedral_angle_1_deg 7.078 r_scangle_it 4.85 r_scbond_it 3.106 r_angle_refined_deg 1.932 r_mcangle_it 1.785 r_mcbond_it 1.095 r_chiral_restr 0.166 r_bond_refined_d 0.025 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5050 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 221
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction MOLREP phasing