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Crystallographic analysis of a chemically modified triosephosphate isomerase from Trypanosoma cruzi with dithiobenzylamine (DTBA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TCD PDB ENTRY 1TCD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 291 5 MICROL OF THE PROTEIN SOLUTION WERE MIXED WITH 5 MICROL OF 2 % POLYETHYLENE GLYCOL 400, 0.1 M HEPES, 2.0M AMMONIUM SULFATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K, PH 7.50. CRYSTAL SOAKED IN
DITHIOBENZYLAMINE
Crystal Properties Matthews coefficient Solvent content 2.18 43.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.206 α = 90 b = 75.337 β = 90 c = 146.427 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 IMAGE PLATE RIGAKU RAXIS IIC MIRRORS 2006-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.15 41.45 91 0.093 10.3 3.4 23141
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 2.15 2.23 96.8 0.316 3.8 3.6
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 1TCD 2.15 41.45 25429 23141 1248 91 0.199 0.196 0.1963 0.25 0.2504 RANDOM 20.788
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] 0.22 -0.35 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.2 r_dihedral_angle_4_deg 18.424 r_dihedral_angle_3_deg 14.881 r_dihedral_angle_1_deg 6.306 r_scangle_it 4.342 r_scbond_it 3.096 r_angle_refined_deg 1.914 r_mcangle_it 1.733 r_mcbond_it 1.588 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.2 r_dihedral_angle_4_deg 18.424 r_dihedral_angle_3_deg 14.881 r_dihedral_angle_1_deg 6.306 r_scangle_it 4.342 r_scbond_it 3.096 r_angle_refined_deg 1.914 r_mcangle_it 1.733 r_mcbond_it 1.588 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.253 r_symmetry_hbond_refined 0.245 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.205 r_chiral_restr 0.133 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3846 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling MOLREP phasing