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Trypanosoma brucei procathepsin B structure solved by Serial Microcrystallography using synchrotron radiation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 310.15 Spontaneous formation of needle-shaped microcrystals in Sf9 cells infected with recombinant baculovirus containing the gene encoding the pre-pro form of Trypanosoma brucei cathepsin B, pH 7.4, Crystallization in vivo within living Sf9 insect cells, temperature 310.15 K as described in Koopmann et al. 2012 Nature Methods
Crystal Properties Matthews coefficient Solvent content 2.79 55.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.42 α = 90 b = 124.42 β = 90 c = 53.77 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 105 PIXEL DECTRIS PILATUS 6M KB mirrors, Si 111 monochromator 2013-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 1.2398 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.3 88.1 99.8 12.3 8881 6448 1 1 31.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.16 99.8 1 12.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.3 88.1 1 8881 6448 305 99.81 0.20162 0.19939 0.2033 0.25069 0.252 RANDOM 37.73
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] 0.92 0.92 -1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.614 r_dihedral_angle_3_deg 16.491 r_dihedral_angle_4_deg 13.717 r_dihedral_angle_1_deg 5.342 r_angle_refined_deg 1.321 r_angle_other_deg 0.85 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.614 r_dihedral_angle_3_deg 16.491 r_dihedral_angle_4_deg 13.717 r_dihedral_angle_1_deg 5.342 r_angle_refined_deg 1.321 r_angle_other_deg 0.85 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2392 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 67
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling