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Plasmodium Falciparum Triosephosphate isomerase (PfTIM) compled to substrate analog glycerol-3-phosphate (G3P).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YDV Dimer of Unbound PfTIM; PDB code 1YDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 295 12% to 20% PEG 1450 in 100mm Sodium acetate, pH 4.5,
VAPOR DIFFUSION, HANGING DROP at 295K
Crystal Properties Matthews coefficient Solvent content 2.26 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.124 α = 90 b = 51.082 β = 91.39 c = 89.549 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 295 IMAGE PLATE MARRESEARCH Mirrors 1999-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 20 96.5 0.115 12.3 5.1 19337 16.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.49 96.4 0.356 4.1 4.8 1824
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 Dimer of Unbound PfTIM; PDB code 1YDV 2.4 20 0.1 17844 1749 92.1 0.179 0.1804 0.216 0.2171 RANDOM 25.5
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] -2.67 1.01 -1.38 4.05
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 5.05 c_scbond_it 3.39 c_mcangle_it 2.8 c_mcbond_it 1.85 c_angle_deg 1.5 c_improper_angle_d 0.97 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3912 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 20
Software Software Software Name Purpose AMoRE phasing CNS refinement DENZO data reduction SCALEPACK data scaling