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Crystal structure of Trypanosoma brucei cathepsin B Y217C/S275C mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 IN CELL 293 In cell crystallization
Crystal Properties Matthews coefficient Solvent content 2.79 55.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.65 α = 90 b = 123.65 β = 90 c = 54.28 γ = 90
Symmetry Space Group P 42 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 PILATUS3 6M 2019-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.35 50 100 0.979 6.9 243 18117
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.37 0.416
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 4hwy 2.35 49.751 18080 922 99.978 0.221 0.2189 0.2276 0.2572 0.2665 30.125
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] 1.22 1.22 -2.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.56 r_dihedral_angle_4_deg 17.574 r_dihedral_angle_3_deg 17.221 r_dihedral_angle_1_deg 7.308 r_lrange_other 5.89 r_lrange_it 5.889 r_scangle_it 4.724 r_scangle_other 4.723 r_mcangle_it 3.454 r_mcangle_other 3.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.56 r_dihedral_angle_4_deg 17.574 r_dihedral_angle_3_deg 17.221 r_dihedral_angle_1_deg 7.308 r_lrange_other 5.89 r_lrange_it 5.889 r_scangle_it 4.724 r_scangle_other 4.723 r_mcangle_it 3.454 r_mcangle_other 3.454 r_scbond_it 3.012 r_scbond_other 3.012 r_mcbond_it 2.188 r_mcbond_other 2.187 r_angle_refined_deg 1.683 r_angle_other_deg 1.237 r_symmetry_nbd_refined 0.287 r_nbd_other 0.19 r_nbd_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.171 r_symmetry_nbd_other 0.169 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.146 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2379 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PHENIX phasing XDS data processing