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The monomerization of Triosephosphate Isomerase from Trypanosoma cruzi
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 VAPOR DIFFUSION 7.5 282 CRYSTALS WERE GROWN AT 9 DEGREES. RESERVOIR SOLUTION OF 100 MM HEPES, PH 7.5, 10% PEG 6000, AND 5% 2-METHYL-2,4-PENTANEDIOL. THE CRYSTALS WERE CRYOPROTECTED BY ADDING PEG 400 30% TO THE RESERVOIR. THEY WERE IMMEDIATELY FROZEN IN LIQUID NITROGEN.
Crystal Properties Matthews coefficient Solvent content 1 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.327 α = 90 b = 77.673 β = 90 c = 43.052 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD MARRESEARCH 2007-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 52.13 99.9 0.05 18.71 4.15 16558 -3.7
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 2.02 100 0.26 3.89 4.21
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 1TCD 2 52.13 15686 835 99.87 0.2137 0.21157 0.2103 0.25693 0.2517 RANDOM 35.952
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] 2.08 -2.56 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.796 r_dihedral_angle_4_deg 21.387 r_dihedral_angle_3_deg 18.793 r_dihedral_angle_1_deg 14.685 r_scangle_it 5.394 r_scbond_it 3.314 r_mcangle_it 2.375 r_angle_refined_deg 1.839 r_mcbond_it 1.376 r_symmetry_vdw_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.796 r_dihedral_angle_4_deg 21.387 r_dihedral_angle_3_deg 18.793 r_dihedral_angle_1_deg 14.685 r_scangle_it 5.394 r_scbond_it 3.314 r_mcangle_it 2.375 r_angle_refined_deg 1.839 r_mcbond_it 1.376 r_symmetry_vdw_refined 0.321 r_nbtor_refined 0.314 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.126 r_symmetry_hbond_refined 0.102 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 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 1809 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing