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Crystal structure of a type II tryparedoxin-dependant peroxidase from Trypanosoma brucei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P5Q PDB ENTRY 2P5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.2 36.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.26 α = 90 b = 32.7 β = 95.92 c = 58.31 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 ADSC CCD MIRRORS 2007-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.1 58 96.2 0.06 25.5 3.9 9469 2
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 2.09 2.15 78.5 0.26 12.2 2.7
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 PDB ENTRY 2P5Q 2.1 58.03 9544 456 98.1 0.208 0.205 0.2038 0.263 0.2582 RANDOM 27.52
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] 1.461 -1.641 -1.412 -0.388
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.078 r_dihedral_angle_4_deg 23.452 r_dihedral_angle_3_deg 15.871 r_dihedral_angle_1_deg 5.949 r_scangle_it 1.711 r_angle_refined_deg 1.114 r_scbond_it 1.085 r_mcangle_it 1.033 r_mcbond_it 0.591 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.078 r_dihedral_angle_4_deg 23.452 r_dihedral_angle_3_deg 15.871 r_dihedral_angle_1_deg 5.949 r_scangle_it 1.711 r_angle_refined_deg 1.114 r_scbond_it 1.085 r_mcangle_it 1.033 r_mcbond_it 0.591 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.201 r_symmetry_vdw_refined 0.194 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_mcangle_other r_scbond_other 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 1295 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing