X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.7
Temperature 293.0
Details 1 uL protein solution (2.8 mg/mL protein, 50 mM Tris, pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 1 mM anthraquinone-2,6-disulfonic acid disodium salt, 7.5 mM GTP) + 0.4 uL well solution (1.5 M sodium formate, 100 mM sodium citrate, pH 4.7, 10 mM dithiothreitol) suspended over 1 mL of well solution, crystals transferred to a soaking solution (3.25 M sodium formate, 100 mM sodium citrate, pH 4.7) containing 1 mM inhibitor, incubated approximately 15 hours at room temperature, and then transferred to a cryo-preservative solution (soaking solution with 25% v/v glycerol) prior to freezing in liquid nitrogen

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.79 α = 90
b = 80.79 β = 90
c = 54.26 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-01-28
Diffraction Radiation
Monochromator Protocol
Si(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1

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
2.62 25.29 98.8 0.042 -- -- 4.7 -- 6117 -- -- 74.73
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)
2.616 2.625 89.9 0.374 -- -- 3.7 62

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
FOURIER SYNTHESIS 2.62 25.29 -- 0.0 -- 6084 304 98.77 -- 0.1644 0.1617 0.2164 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 2.62 2.93 -- 96 1589 0.1895 0.2609 -- 98.77
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 71.85
Anisotropic B[1][1] 1.4624
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.4624
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.9248
RMS Deviations
Key Refinement Restraint Deviation
t_omega_torsion 3.07
t_angle_deg 1.2
t_other_torsion 19.96
t_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.337
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1260
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 72

Software

Software
Software Name Purpose
PROCESS data scaling
BUSTER-TNT refinement version: BUSTER 2.11.5
PDB_EXTRACT data extraction version: 3.15
PROCESS data reduction
BUSTER-TNT phasing