X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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 SLAC LCLS BEAMLINE CXI 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_angle_refined_deg 1.54
r_chiral_restr 0.122
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_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

Software
Software Name Purpose
CXI data collection version: DAQ
MOLREP phasing
REFMAC refinement version: 5.6.0117
CrystFEL data reduction
CrystFEL data scaling