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Crystal structure of the F96S mutant of Plasmodium falciparum triosephosphate isomerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O5X PDB ENTRY 1O5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 0.1 M SODIUM ACETATE PH 4.0-5.5, PEG 1450 8-24%
Crystal Properties Matthews coefficient Solvent content 2.1 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.423 α = 90 b = 50.698 β = 92.17 c = 89.188 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 DIP-2040B 2006-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU SPring-8 BL44XU
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 1.4 50 96.3 0.05 40.5 3.3 90838 13.5
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 1.4 1.45 93.9 0.24 7 3.2
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1O5X 1.4 36.76 86241 4556 96.18 0.16628 0.16511 0.1633 0.18828 0.1863 RANDOM 14.788
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 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.889 r_dihedral_angle_4_deg 12.039 r_dihedral_angle_3_deg 11.077 r_dihedral_angle_1_deg 5.519 r_scangle_it 2.695 r_scbond_it 1.747 r_angle_refined_deg 1.088 r_mcangle_it 0.997 r_mcbond_it 0.638 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.889 r_dihedral_angle_4_deg 12.039 r_dihedral_angle_3_deg 11.077 r_dihedral_angle_1_deg 5.519 r_scangle_it 2.695 r_scbond_it 1.747 r_angle_refined_deg 1.088 r_mcangle_it 0.997 r_mcbond_it 0.638 r_nbtor_refined 0.303 r_nbd_refined 0.185 r_symmetry_vdw_refined 0.165 r_symmetry_hbond_refined 0.127 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.073 r_bond_refined_d 0.007 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3882 Nucleic Acid Atoms Solvent Atoms 660 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CCP4 phasing