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Crystal structure of Trypanosoma brucei cathepsin B R91C/T223C 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 2.89 57.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.1 α = 90 b = 125.1 β = 90 c = 55.02 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 2.3 50 100 0.99 7.7 558 20010
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 2.3 2.32 0.374
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 2.3 46.764 19956 1006 99.9 0.224 0.2213 0.2293 0.2728 0.2757 32.816
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] 0.755 0.755 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.187 r_dihedral_angle_4_deg 20.087 r_dihedral_angle_3_deg 16.35 r_dihedral_angle_1_deg 7.268 r_lrange_it 5.8 r_lrange_other 5.794 r_scangle_it 4.571 r_scangle_other 4.57 r_mcangle_it 3.528 r_mcangle_other 3.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.187 r_dihedral_angle_4_deg 20.087 r_dihedral_angle_3_deg 16.35 r_dihedral_angle_1_deg 7.268 r_lrange_it 5.8 r_lrange_other 5.794 r_scangle_it 4.571 r_scangle_other 4.57 r_mcangle_it 3.528 r_mcangle_other 3.527 r_scbond_it 2.858 r_scbond_other 2.856 r_mcbond_it 2.247 r_mcbond_other 2.239 r_angle_refined_deg 1.685 r_angle_other_deg 1.233 r_symmetry_nbtor_refined 0.25 r_nbd_other 0.238 r_nbd_refined 0.184 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.133 r_symmetry_nbd_refined 0.106 r_symmetry_xyhbond_nbd_refined 0.095 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.071 r_bond_refined_d 0.008 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 68 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PHENIX phasing XDS data processing