X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 277.0
Details 1 uL 20 mg/mL lyophilized toxin in 2 mM hydrochloric acid + 1 uL reservoir (0.1 M Tris-HCl, pH 7.5, 2% v/v dioxane, 56-60% v/v MPD) against 500 uL reservoir (rod-shaped crystals appeared after 24 hours, grew to 0.5 x 0.1 x 0.1 mm), VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.73 α = 90
b = 48.73 β = 90
c = 63.24 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944 -- 2012-05-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54 -- --

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
1.58 35.1 97.2 0.039 -- -- 3.21 8454 8431 0.0 0.0 11.76
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)
1.58 1.64 95.6 0.325 -- 1.5 1.54 --

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 1.8 35.1 0.0 0.0 -- 7763 397 96.75 -- 0.18593 0.18511 0.20192 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 1.8 1.847 -- 23 469 0.251 0.375 -- 86.77
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.213
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.01
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 2.671
r_dihedral_angle_1_deg 6.504
r_dihedral_angle_2_deg 40.395
r_chiral_restr 0.298
r_dihedral_angle_3_deg 13.215
r_gen_planes_refined 0.013
r_bond_refined_d 0.027
r_dihedral_angle_4_deg 8.025
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 501
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 45

Software

Software
Software Name Purpose
CrystalClear data collection
PHASER phasing
REFMAC refinement version: 5.6.0117
CrystalClear data reduction
CrystalClear data scaling