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Crystal structure of Q64E mutant of Triosephosphate isomerase from Plasmodium falciparum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 28% PEG 1450, 100mM HEPES, 10mM calcium chloride, 0.5mM DTT, 0.5mM sodium azide
Crystal Properties Matthews coefficient Solvent content 1.94 36.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.02 α = 90 b = 75.35 β = 97.72 c = 74.13 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 MAR scanner 345 mm plate 2013-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.541
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.526 75.35 97.2 0.156 0.187 0.101 5.6 3.2 14204 14204 40
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.51 2.65 81.4 0.441 0.441 0.298 2.3 3 1734
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 1O5X 2.53 73.57 13474 714 98.5 0.232 0.2288 0.2347 0.2927 0.2902 RANDOM 23.718
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] -0.92 -0.63 -0.34 1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.058 r_dihedral_angle_4_deg 13.232 r_dihedral_angle_3_deg 12.491 r_dihedral_angle_1_deg 5.8 r_angle_refined_deg 1.07 r_angle_other_deg 0.87 r_mcangle_it 0.714 r_mcbond_it 0.407 r_mcbond_other 0.406 r_chiral_restr 0.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.058 r_dihedral_angle_4_deg 13.232 r_dihedral_angle_3_deg 12.491 r_dihedral_angle_1_deg 5.8 r_angle_refined_deg 1.07 r_angle_other_deg 0.87 r_mcangle_it 0.714 r_mcbond_it 0.407 r_mcbond_other 0.406 r_chiral_restr 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3667 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing