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Crystal Structure of Human Peroxiredoxin I in complex with Sulfiredoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QQ2 1QQ2, 1XW3 experimental model PDB 1XW3 1QQ2, 1XW3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 14% PEG8000, 16% Ethylene glycol, 100 mM Hepes pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 44.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.921 α = 90 b = 85.045 β = 90 c = 130.832 γ = 90
Symmetry Space Group P 21 21 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 4 2005-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 1.0 NSLS X8C
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 2.6 51.85 100 0.062 15.8 6.9 19543 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.7 100 0.385 4.7 7
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 1QQ2, 1XW3 2.6 43.52 18499 995 99.94 0.24232 0.23873 0.2353 0.30837 0.3064 RANDOM 26.902
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] 0.08 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.253 r_dihedral_angle_4_deg 21.665 r_dihedral_angle_3_deg 21.526 r_dihedral_angle_1_deg 7.047 r_scangle_it 2.133 r_angle_refined_deg 1.504 r_scbond_it 1.324 r_mcangle_it 0.965 r_mcbond_it 0.534 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.253 r_dihedral_angle_4_deg 21.665 r_dihedral_angle_3_deg 21.526 r_dihedral_angle_1_deg 7.047 r_scangle_it 2.133 r_angle_refined_deg 1.504 r_scbond_it 1.324 r_mcangle_it 0.965 r_mcbond_it 0.534 r_nbtor_refined 0.323 r_symmetry_vdw_refined 0.264 r_symmetry_hbond_refined 0.264 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 4465 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement CBASS data collection d*TREK data reduction d*TREK data scaling PHASER phasing