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Crystal structure of triosephosphate isomerase from Leishmania orientalis at 1.45 angstroms resolution with an arsenic atom bound at Cys57
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CI1 Chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.7 291.15 18% PEG 8000 in 0.2M calcium acetate hydrate and 0.1M sodium cacodylate trihydrate pH5.9
Crystal Properties Matthews coefficient Solvent content 2.29 46.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.7 α = 90 b = 79.353 β = 101.24 c = 83.114 γ = 90
Symmetry Space Group P 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 PIXEL DECTRIS EIGER2 X 9M a pair of K-B mirrors 2022-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.99987 NSRRC TPS 05A
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 1.45 50 98.6 0.226 0.247 0.099 0.979 6.4 5.9 87903 10.69
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 1.45 1.48 96.6 1.316 1.472 0.65 0.517 5.3 4.1
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 1.45 19.74 83436 4421 98.41 0.1636 0.16215 0.1622 0.19047 0.1906 RANDOM 13.47
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 12.756 r_dihedral_angle_1_deg 6.552 r_dihedral_angle_2_deg 6.296 r_long_range_B_refined 4.852 r_long_range_B_other 4.712 r_scangle_other 3.916 r_scbond_it 2.64 r_scbond_other 2.639 r_mcangle_it 1.969 r_mcangle_other 1.969
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.756 r_dihedral_angle_1_deg 6.552 r_dihedral_angle_2_deg 6.296 r_long_range_B_refined 4.852 r_long_range_B_other 4.712 r_scangle_other 3.916 r_scbond_it 2.64 r_scbond_other 2.639 r_mcangle_it 1.969 r_mcangle_other 1.969 r_angle_refined_deg 1.789 r_mcbond_it 1.353 r_mcbond_other 1.349 r_angle_other_deg 0.576 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 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 3723 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling DENZO data reduction PHASER phasing