4HWY

Trypanosoma brucei procathepsin B solved from 40 fs free-electron laser pulse data by serial femtosecond X-ray crystallography


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MORPDB entry 3MOR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Crystallization in vivo within living SF9 insect cells7.4310.15Spontaneous 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 coefficientSolvent content
2.8857.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.4α = 90
b = 125.4β = 90
c = 54.56γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELCornell-SLAC Pixel Array Detector2011-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE CXI1.32SLAC LCLSCXI

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.1201002596925969
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.175100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3MOR2.188.672464824648132199.990.183350.181810.21308RANDOM46.244
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]
0.360.36-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.25
r_dihedral_angle_4_deg21.773
r_dihedral_angle_3_deg15.671
r_dihedral_angle_1_deg6.964
r_angle_refined_deg1.54
r_chiral_restr0.122
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.25
r_dihedral_angle_4_deg21.773
r_dihedral_angle_3_deg15.671
r_dihedral_angle_1_deg6.964
r_angle_refined_deg1.54
r_chiral_restr0.122
r_bond_refined_d0.013
r_gen_planes_refined0.012
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 AtomsNumber
Protein Atoms2386
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms67

Software

Software
Software NamePurpose
CXIdata collection
MOLREPphasing
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling