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Crystal structure of human peroxiredoxin 4 (thioredoxin peroxidase)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QMV PDB entry 1QMV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M HEPES pH 7.5, 10% PEG 10000, 8% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.93 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.188 α = 90 b = 138.776 β = 104.52 c = 108.989 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 MARMOSAIC 225 mm CCD 2007-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.95370 SLS X10SA
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 1.8 50 99.01 0.103 0.12 10.1 3.8 255385 252831 2 20.6
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) 1.8 1.9 98.3 0.578 0.675 2.3 3.8 36549
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1QMV 1.8 50 252831 252831 12684 99.01 0.15277 0.15277 0.15108 0.1626 0.18454 0.1936 RANDOM 14.209
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] -1.14 -0.48 0.33 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.436 r_dihedral_angle_4_deg 15.297 r_dihedral_angle_3_deg 11.243 r_scangle_it 7.343 r_dihedral_angle_1_deg 6.237 r_scbond_it 5.02 r_mcangle_it 3.438 r_mcbond_it 2.657 r_angle_refined_deg 1.327 r_angle_other_deg 0.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.436 r_dihedral_angle_4_deg 15.297 r_dihedral_angle_3_deg 11.243 r_scangle_it 7.343 r_dihedral_angle_1_deg 6.237 r_scbond_it 5.02 r_mcangle_it 3.438 r_mcbond_it 2.657 r_angle_refined_deg 1.327 r_angle_other_deg 0.919 r_mcbond_other 0.789 r_symmetry_vdw_other 0.255 r_nbd_refined 0.196 r_nbd_other 0.195 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.152 r_xyhbond_nbd_refined 0.15 r_symmetry_vdw_refined 0.126 r_chiral_restr 0.086 r_nbtor_other 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15435 Nucleic Acid Atoms Solvent Atoms 2183 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling PHASER phasing