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Leishmania donovani ISP2 in complex with bovine alpha-chymotrypsin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9H6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.15 M DL-Malic acid 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.013 α = 90 b = 90.799 β = 90 c = 96.645 γ = 90
Symmetry Space Group P 21 21 21
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 0.97499 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 48.37 100 0.199 0.201 0.027 0.999 11.5 54 53201
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 2.03 100 2.082 2.103 0.291 0.875 0.6 51.5
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 48.369 53114 2682 99.889 0.218 0.2156 0.2188 0.2738 0.2754 48.305
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] 4.69 -0.376 -4.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.543 r_dihedral_angle_3_deg 13.764 r_dihedral_angle_2_deg 9.888 r_lrange_it 8.246 r_lrange_other 8.246 r_dihedral_angle_1_deg 7.626 r_scangle_it 6.744 r_scangle_other 6.744 r_mcangle_it 6.23 r_mcangle_other 6.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.543 r_dihedral_angle_3_deg 13.764 r_dihedral_angle_2_deg 9.888 r_lrange_it 8.246 r_lrange_other 8.246 r_dihedral_angle_1_deg 7.626 r_scangle_it 6.744 r_scangle_other 6.744 r_mcangle_it 6.23 r_mcangle_other 6.23 r_scbond_it 4.941 r_scbond_other 4.941 r_mcbond_it 4.787 r_mcbond_other 4.787 r_angle_refined_deg 1.549 r_angle_other_deg 0.518 r_symmetry_nbd_refined 0.266 r_symmetry_nbd_other 0.202 r_nbd_refined 0.199 r_nbd_other 0.191 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_refined 0.124 r_ncsr_local_group_1 0.111 r_symmetry_nbtor_other 0.09 r_ncsr_local_group_2 0.077 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.015 r_bond_refined_d 0.008 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 5557 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement xia2.multiplex data reduction Aimless data scaling PHASER phasing