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Tryparedoxin peroxidase (TXNPX) from trypanosoma cruzi in the reduced state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E2Y PDB ENTRY 1E2Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 100MM EDTA, 15% PEG3350, 10% GLYCEROL, 100MM TRISHCL PH7.5, 100MM DTT, 0.25% DMSO, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.09 60.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.555 α = 90 b = 87.018 β = 102.77 c = 127.144 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 287 CCD ADSC QUANTUM 210 2002-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.8 30 99.9 0.132 3.72 66025 66025
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 99.7 0.21 6.44 3.63
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 (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 1E2Y 2.8 29.97 62685 62685 3350 99.81 0.16361 0.16195 0.167 0.19518 0.1944 RANDOM 30.852
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] -0.01 -0.14 0.15 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.839 r_dihedral_angle_3_deg 20.56 r_dihedral_angle_4_deg 13.286 r_dihedral_angle_1_deg 6.619 r_mcangle_it 3.606 r_scbond_it 3.463 r_mcbond_it 2.268 r_mcbond_other 2.268 r_angle_refined_deg 1.83 r_angle_other_deg 1.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.839 r_dihedral_angle_3_deg 20.56 r_dihedral_angle_4_deg 13.286 r_dihedral_angle_1_deg 6.619 r_mcangle_it 3.606 r_scbond_it 3.463 r_mcbond_it 2.268 r_mcbond_other 2.268 r_angle_refined_deg 1.83 r_angle_other_deg 1.695 r_chiral_restr 0.111 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.009 r_gen_planes_other 0.007 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15380 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection