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Crystal structure of T75V 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 6.5 296 20% PEG 1450, 100 mM MES buffer, 10 mM Calcium chloride, 0.5 mM EDTA, 0.5 mM DTT, 0.5 mM sodium azide
Crystal Properties Matthews coefficient Solvent content 1.97 37.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.21 α = 90 b = 76.02 β = 97.47 c = 74.36 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 2014-04-10 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 1.859 73.73 99.8 0.056 0.061 0.025 22.2 5.6 36392 36392
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 1.86 1.96 98.4 0.156 0.156 0.075 4.7 5.2 5211
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 1.86 73.73 34547 1816 99.74 0.134 0.1314 0.1457 0.1824 0.1924 RANDOM 11.586
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] 0.22 -0.02 -0.16 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.944 r_dihedral_angle_3_deg 11.758 r_dihedral_angle_4_deg 11.258 r_dihedral_angle_1_deg 6.47 r_angle_refined_deg 1.802 r_mcangle_it 1.303 r_angle_other_deg 1.033 r_mcbond_it 0.896 r_mcbond_other 0.89 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.944 r_dihedral_angle_3_deg 11.758 r_dihedral_angle_4_deg 11.258 r_dihedral_angle_1_deg 6.47 r_angle_refined_deg 1.802 r_mcangle_it 1.303 r_angle_other_deg 1.033 r_mcbond_it 0.896 r_mcbond_other 0.89 r_chiral_restr 0.111 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3859 Nucleic Acid Atoms Solvent Atoms 483 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing