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Crystal structure of T75C 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 7.5 296 16% PEG 1450, 100mM HEPES, 10 mM calcium chloride, 0.5 mM EDTA, 0.5 mM DTT, 0.5 mM sodium azide
Crystal Properties Matthews coefficient Solvent content 2.01 38.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.36 α = 90 b = 76.88 β = 97.79 c = 74.48 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 CCD MARMOSAIC 225 mm CCD 2014-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95372 ESRF BM14
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 1.8 73.792 100 0.058 0.066 0.032 12.6 4.1 40771 40771
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 1.8 1.9 100 0.593 0.593 0.336 1.2 4.1 5902
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 1.8 73.79 38709 2041 99.94 0.2087 0.2061 0.2126 0.2581 0.2608 RANDOM 29.867
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] 1.19 0.26 -0.35 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.12 r_dihedral_angle_3_deg 13.21 r_dihedral_angle_4_deg 12.102 r_dihedral_angle_1_deg 6.784 r_mcangle_it 3.878 r_mcbond_it 2.972 r_mcbond_other 2.972 r_angle_refined_deg 1.85 r_angle_other_deg 1.054 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.12 r_dihedral_angle_3_deg 13.21 r_dihedral_angle_4_deg 12.102 r_dihedral_angle_1_deg 6.784 r_mcangle_it 3.878 r_mcbond_it 2.972 r_mcbond_other 2.972 r_angle_refined_deg 1.85 r_angle_other_deg 1.054 r_chiral_restr 0.107 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3526 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing