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Trypanosoma brucei procathepsin B solved from 40 fs free-electron laser pulse data by serial femtosecond X-ray crystallography
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MOR PDB entry 3MOR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Crystallization in vivo within living SF9 insect cells 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 310.15K
Crystal Properties Matthews coefficient Solvent content 2.88 57.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.4 α = 90 b = 125.4 β = 90 c = 54.56 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 293 PIXEL Cornell-SLAC Pixel Array Detector 2011-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.32 SLAC LCLS CXI
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 2.1 20 100 25969 25969
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 2.1 2.175 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB entry 3MOR 2.1 88.67 24648 24648 1321 99.99 0.18335 0.18181 0.1787 0.21308 0.2103 RANDOM 46.244
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] 0.36 0.36 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.25 r_dihedral_angle_4_deg 21.773 r_dihedral_angle_3_deg 15.671 r_dihedral_angle_1_deg 6.964 r_angle_refined_deg 1.54 r_chiral_restr 0.122 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.25 r_dihedral_angle_4_deg 21.773 r_dihedral_angle_3_deg 15.671 r_dihedral_angle_1_deg 6.964 r_angle_refined_deg 1.54 r_chiral_restr 0.122 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2386 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 67
Software Software Software Name Purpose CXI data collection MOLREP phasing REFMAC refinement CrystFEL data reduction CrystFEL data scaling