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Leishmania donovani ISP2 in complex with bovine trypsin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Leishmania major ISP2 - bovine chymotrypsin complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 298 20 % w/v PEG 6000 0.1 M Sodium citrate 4.0 0.2 M Lithium chloride
Crystal Properties Matthews coefficient Solvent content 2.13 42.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.697 α = 90 b = 191.794 β = 90 c = 45.282 γ = 90
Symmetry Space Group P 21 21 2
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 XE 16M 2022-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.588 60.16 100 0.282 0.286 0.045 0.998 8.9 40.3 47428
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 2.6 2.64 100 1.934 1.962 0.328 0.89 0.7 35.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.588 59.942 47265 750 99.232 0.199 0.1975 0.1988 0.2741 0.2754 69.709
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] -7.819 5.057 2.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.945 r_lrange_it 13.189 r_lrange_other 13.186 r_dihedral_angle_6_deg 12.966 r_scangle_it 11.656 r_scangle_other 11.655 r_dihedral_angle_2_deg 11.242 r_mcangle_it 10.29 r_mcangle_other 10.29 r_scbond_it 8.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.945 r_lrange_it 13.189 r_lrange_other 13.186 r_dihedral_angle_6_deg 12.966 r_scangle_it 11.656 r_scangle_other 11.655 r_dihedral_angle_2_deg 11.242 r_mcangle_it 10.29 r_mcangle_other 10.29 r_scbond_it 8.834 r_scbond_other 8.83 r_mcbond_it 7.877 r_mcbond_other 7.874 r_dihedral_angle_1_deg 7.625 r_angle_refined_deg 1.769 r_angle_other_deg 0.598 r_symmetry_nbd_refined 0.28 r_nbd_other 0.219 r_nbd_refined 0.198 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.175 r_xyhbond_nbd_refined 0.17 r_ncsr_local_group_6 0.1 r_ncsr_local_group_8 0.1 r_symmetry_xyhbond_nbd_other 0.099 r_ncsr_local_group_11 0.096 r_ncsr_local_group_9 0.094 r_symmetry_nbtor_other 0.093 r_chiral_restr 0.085 r_ncsr_local_group_10 0.085 r_ncsr_local_group_7 0.08 r_ncsr_local_group_2 0.075 r_ncsr_local_group_1 0.072 r_ncsr_local_group_4 0.07 r_ncsr_local_group_3 0.065 r_ncsr_local_group_5 0.062 r_ncsr_local_group_12 0.057 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10465 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement xia2 data reduction SCALEPACK data scaling PHASER phasing