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Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi Complexed with Chalepin, a Coumarin Derivative Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Holo-D-Glyceraldehyde-3-phosphate dehydrogenase from T. cruzi solved at 2.8 A resolution by Souza et al., FEBS Letters, 424 (1998), 131-135.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 295 16% PEG 8000, 0.1M calcium acetate, 0.1M sodium cacodylate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.338 47.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.08 α = 90 b = 84.97 β = 96.32 c = 105.24 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 IMAGE PLATE RIGAKU RAXIS IIC 1998-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
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 1.95 44.72 77.9 0.107 6.78 2.4 81630 81630 22.48
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) 1.95 2.02 38.1 0.483 1.1 1.6 3980
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Holo-D-Glyceraldehyde-3-phosphate dehydrogenase from T. cruzi solved at 2.8 A resolution by Souza et al., FEBS Letters, 424 (1998), 131-135. 1.95 15 81471 81471 2478 100 0.201 0.1969 0.28 0.2669 RANDOM 31.81
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]
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 3 p_mcangle_it 2.6 p_scbond_it 2.1 p_mcbond_it 1.8 p_bond_d 0.15 p_planar_d 0.041 p_angle_d 0.04 o_bond_d_na o_bond_d_prot o_angle_d_na
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 3 p_mcangle_it 2.6 p_scbond_it 2.1 p_mcbond_it 1.8 p_bond_d 0.15 p_planar_d 0.041 p_angle_d 0.04 o_bond_d_na o_bond_d_prot o_angle_d_na o_angle_d_prot o_angle_deg o_angle_deg_na o_angle_deg_prot o_dihedral_angle_d o_dihedral_angle_d_na o_dihedral_angle_d_prot o_improper_angle_d o_improper_angle_d_na o_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10982 Nucleic Acid Atoms Solvent Atoms 937 Heterogen Atoms 23
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling