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Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi in complex with the irreversible iodoacetate inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K3T PDB ENTRY 1K3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 291 18% PEG 8000, 0.1M calcium acetate, 0.1M sodium cacodylate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.21 44.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.755 α = 90 b = 83.713 β = 96.44 c = 105.611 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 MAR CCD 130 mm 2007-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.4250 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 38.9 96.9 0.135 0.135 2.8 3.6 59362 58629 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 96.9 0.135 0.135 2.8 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 1K3T 2.3 38.1 59362 55620 2987 96.48 0.18956 0.1862 0.1854 0.25166 0.2481 RANDOM 19.905
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] -0.01 0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.769 r_dihedral_angle_4_deg 18.642 r_dihedral_angle_3_deg 16.649 r_dihedral_angle_1_deg 6.64 r_scangle_it 2.519 r_scbond_it 1.638 r_angle_refined_deg 1.436 r_mcangle_it 1.091 r_mcbond_it 0.644 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.769 r_dihedral_angle_4_deg 18.642 r_dihedral_angle_3_deg 16.649 r_dihedral_angle_1_deg 6.64 r_scangle_it 2.519 r_scbond_it 1.638 r_angle_refined_deg 1.436 r_mcangle_it 1.091 r_mcbond_it 0.644 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.183 r_symmetry_hbond_refined 0.161 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 10936 Nucleic Acid Atoms Solvent Atoms 1005 Heterogen Atoms 182
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling MOLREP phasing PHENIX refinement