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Crystal structure of reduced tryparedoxin peroxidase from leishmania major at 2.34 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TUE PDB ENTRY 3TUE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 20% PEG 3350, 0.2M NaSO4, 0.1M TRIS-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.63 53.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.811 α = 90 b = 226.203 β = 90 c = 91.719 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 100 PIXEL DECTRIS PILATUS 2M 2013-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1 ELETTRA 5.2R
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 2.34 113.1 98.9 0.162 10.26 49646 49113 -3 41.222
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.34 2.48 94.7 1.07 1.189 1.65
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 3TUE 2.34 113.1 49112 2489 98.91 0.1963 0.1936 0.1807 0.2467 0.2303 RANDOM 27.4724
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] 0.05 0.52 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.493 r_dihedral_angle_3_deg 16.816 r_dihedral_angle_4_deg 13.675 r_dihedral_angle_1_deg 6.356 r_scangle_it 3.301 r_scbond_it 2.009 r_angle_refined_deg 1.53 r_mcangle_it 1.229 r_mcbond_it 0.653 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.493 r_dihedral_angle_3_deg 16.816 r_dihedral_angle_4_deg 13.675 r_dihedral_angle_1_deg 6.356 r_scangle_it 3.301 r_scbond_it 2.009 r_angle_refined_deg 1.53 r_mcangle_it 1.229 r_mcbond_it 0.653 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7711 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 67
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling