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thioredoxin peroxidase B from red blood cells
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PRX PDB ENTRY 1PRX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 16 % (V/V) PEG 400, 100 MM TRIS-HCL, PH 7.5, 10 % (V/V) 2-PROPANOL, 10 MM DITHIOERYTHREITOL
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.88 α = 90 b = 107.03 β = 110.87 c = 119.5 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 MARRESEARCH 1998-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 1.7 20 99.6 0.057 18.8 4.2 228010 34.1
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 1.7 1.73 93.6 0.493 1.7 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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PRX 1.7 20 225682 2287 98.6 0.192 0.1793 0.256 RANDOM 32.7
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] -7.341 -1.201 18.791 -11.027
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 26.9 p_staggered_tor 14.3 p_scangle_it 5.849 p_scbond_it 4.675 p_planar_tor 4.2 p_mcangle_it 3.071 p_mcbond_it 2.467 p_multtor_nbd 0.246 p_singtor_nbd 0.173 p_chiral_restr 0.146
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 26.9 p_staggered_tor 14.3 p_scangle_it 5.849 p_scbond_it 4.675 p_planar_tor 4.2 p_mcangle_it 3.071 p_mcbond_it 2.467 p_multtor_nbd 0.246 p_singtor_nbd 0.173 p_chiral_restr 0.146 p_xyhbond_nbd 0.122 p_planar_d 0.031 p_angle_d 0.027 p_plane_restr 0.022 p_bond_d 0.011 p_angle_deg p_hb_or_metal_coord p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15440 Nucleic Acid Atoms Solvent Atoms 2194 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing MOLREP phasing REFMAC refinement