☰ Navigation Tabs
The structure of tryparedoxin peroxidase I from Leishmania major
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 8 293 22% PEG 3350, 0.1 M BIS-TRIS PROPANE, 0.2 M KSCN, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 45.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.977 α = 90 b = 212.385 β = 90 c = 90.948 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 225 mm CCD 2011-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 3 106 99.9 0.15 7.3 2.9 21162
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 3 3.11 99.2 0.518 1.84 2.6
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 1E2Y 3 106 21162 1143 99.84 0.19889 0.19709 0.1945 0.23342 0.2295 RANDOM 36.861
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] 0.12 -1.29 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.115 r_dihedral_angle_3_deg 17.668 r_dihedral_angle_4_deg 16.665 r_dihedral_angle_1_deg 5.379 r_angle_refined_deg 1.02 r_chiral_restr 0.085 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.115 r_dihedral_angle_3_deg 17.668 r_dihedral_angle_4_deg 16.665 r_dihedral_angle_1_deg 5.379 r_angle_refined_deg 1.02 r_chiral_restr 0.085 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6484 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction MOLREP phasing REFMAC refinement SCALEPACK data scaling