X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Crystallization in Vivo Within Living Sf9 Insect Cells
pH 7.4
Temperature 310.15
Details 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 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 # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL Cornell-SLAC Pixel Array Detector -- 2011-02-01
Diffraction Radiation
Monochromator Protocol
CXI SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
Free-electron laser LCLS OTHER 1.32 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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
2.1 20 100.0 -- -- -- -- 25969 25969 0.0 0.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.1 2.175 100.0 -- -- -- -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.1 88.67 -- -- 24648 24648 1321 99.99 -- 0.18335 0.18181 0.21308 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.1 2.155 -- 90 1612 0.317 0.368 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.244
Anisotropic B[1][1] 0.36
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.72
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.012
r_chiral_restr 0.122
r_dihedral_angle_4_deg 21.773
r_dihedral_angle_3_deg 15.671
r_dihedral_angle_2_deg 33.25
r_dihedral_angle_1_deg 6.964
r_angle_refined_deg 1.54
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2386
Nucleic Acid Atoms 0
Heterogen Atoms 67
Solvent Atoms 98

Software

Computing
Computing Package Purpose
CXI DAQ Data Collection
CrystFEL Data Reduction (intensity integration)
CrystFEL Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
MOLREP model building
CXI version: DAQ data collection