☰ Navigation Tabs
Crystal structure of peroxiredoxin Ahp1 from Saccharomyces cerevisiae in oxidized form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TP9 PDB ENTRY 1TP9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 289 25% polyethylene glycol monomethyl ether 2000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.12 42.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.978 α = 90 b = 130.624 β = 104.27 c = 67.678 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 CCD ADSC QUANTUM 315r 2010-12-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9793 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 50 97.2 0.174 0.174 4.718 4.1 25277 25277 -3 39.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 98.9 0.442 0.442 3.028 4 1263
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1TP9 2.4 46.3 23926 1272 96.05 0.23789 0.23612 0.2347 0.27096 0.2693 RANDOM 35.198
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] 1.09 1.64 -1.29 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.078 r_dihedral_angle_3_deg 15.582 r_dihedral_angle_4_deg 9.506 r_dihedral_angle_1_deg 5.943 r_scangle_it 3.338 r_scbond_it 1.906 r_mcangle_it 1.79 r_angle_refined_deg 1.249 r_mcbond_it 1.108 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.078 r_dihedral_angle_3_deg 15.582 r_dihedral_angle_4_deg 9.506 r_dihedral_angle_1_deg 5.943 r_scangle_it 3.338 r_scbond_it 1.906 r_mcangle_it 1.79 r_angle_refined_deg 1.249 r_mcbond_it 1.108 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5328 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling