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Crystal structure of triosephosphate isomerase from Leishmania orientalis at 1.88A with an arsenic ion bound at Cys57
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold I2APN2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.9 291.15 Equal volumes (1.0 microliter) of enzyme (24.2 mg/ml in 50 mM potassium phosphate buffer, pH 8.0, containing 50 mM KCl, 5 mM DTT, and 10% glycerol) and precipitant (PEG8000 18% w/v in 0.2 mM calcium acetate hydrate, 0.1 M and sodium cacodylate trihydrate, pH 5.9)
Crystal Properties Matthews coefficient Solvent content 2.57 52.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.44 α = 90 b = 76.45 β = 101.14 c = 94.94 γ = 90
Symmetry Space Group C 1 2 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 MAR CCD 165 mm spherical mirror for CM and toroidal mirror for M 2015-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLRI BEAMLINE BL7.2W 1.5500 SLRI BL7.2W
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.88 21.56 98.6 0.082 0.101 0.059 0.991 11.9 2.8 46160 6.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.92 81.2 0.549 0.682 0.399 0.598 2.4 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 1.88 19.98 43811 2354 99.06 0.17366 0.17148 0.1825 0.21377 0.2183 RANDOM 16.047
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.959 r_dihedral_angle_1_deg 7.052 r_dihedral_angle_2_deg 5.926 r_long_range_B_refined 4.584 r_long_range_B_other 4.322 r_scangle_other 2.966 r_scbond_it 1.897 r_scbond_other 1.897 r_mcangle_it 1.881 r_mcangle_other 1.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.959 r_dihedral_angle_1_deg 7.052 r_dihedral_angle_2_deg 5.926 r_long_range_B_refined 4.584 r_long_range_B_other 4.322 r_scangle_other 2.966 r_scbond_it 1.897 r_scbond_other 1.897 r_mcangle_it 1.881 r_mcangle_other 1.881 r_angle_refined_deg 1.564 r_mcbond_it 1.321 r_mcbond_other 1.32 r_angle_other_deg 0.517 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3712 Nucleic Acid Atoms Solvent Atoms 491 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement pointless data scaling MOSFLM data reduction PHASER phasing