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Trypanosomatid-specific protein of unknown function
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold3 run Oct 2024
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 0.1 M K2HPO4, 0.1 M Tris pH 8, 30% PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.84 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.225 α = 90 b = 71.647 β = 94.616 c = 67.084 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 ADSC QUANTUM 210 2004-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1
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 2.42 45.714 88.8 0.099 0.118 0.062 0.996 8.3 3.3 17796
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 2.42 2.51 40.3 0.482 0.629 0.398 0.702 1.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AlphaFold3-generated model, from run in Oct 2024 2.45 45.714 17576 908 91.115 0.204 0.2025 0.2076 0.231 0.2291 43.325
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] -0.34 -0.368 0.188 0.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.856 r_dihedral_angle_4_deg 26.192 r_dihedral_angle_3_deg 19.945 r_lrange_it 8.004 r_lrange_other 8 r_dihedral_angle_1_deg 7.929 r_scangle_it 5.379 r_scangle_other 5.377 r_mcangle_it 4.579 r_mcangle_other 4.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.856 r_dihedral_angle_4_deg 26.192 r_dihedral_angle_3_deg 19.945 r_lrange_it 8.004 r_lrange_other 8 r_dihedral_angle_1_deg 7.929 r_scangle_it 5.379 r_scangle_other 5.377 r_mcangle_it 4.579 r_mcangle_other 4.578 r_scbond_it 3.175 r_scbond_other 3.174 r_mcbond_it 2.79 r_mcbond_other 2.786 r_angle_refined_deg 2.15 r_angle_other_deg 1.551 r_nbd_refined 0.241 r_symmetry_nbd_refined 0.22 r_symmetry_nbd_other 0.202 r_nbd_other 0.199 r_xyhbond_nbd_refined 0.198 r_metal_ion_refined 0.174 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.149 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.089 r_ncsr_local_group_1 0.082 r_gen_planes_other 0.02 r_bond_other_d 0.018 r_bond_refined_d 0.016 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2662 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing DENZO data reduction