X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Sitting Drop
pH 6.8
Temperature 277.0
Details 15-20% isopropanol, 0.2 M sodium citrate, 0.5% N,N-dimethyldodecylamine-N-oxide, pH 6.8, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.15 α = 90
b = 64.15 β = 90
c = 275.46 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2010-01-31
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4C 0.979 NSLS X4C

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
2.35 47.53 99.7 0.122 -- -- 9.1 28709 28628 -- -3.0 59.372
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)
2.346 2.49 99.5 0.012 -- 2.01 -- --

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
SAD 2.346 43.239 -- 1.99 28559 28559 1288 99.51 -- 0.2286 0.2272 0.2556 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 2.346 2.4404 -- 91 3000 0.3239 0.3397 -- 99.0
X Ray Diffraction 2.4404 2.5514 -- 109 3011 0.3135 0.3478 -- 100.0
X Ray Diffraction 2.5514 2.6859 -- 147 2980 0.2768 0.3267 -- 100.0
X Ray Diffraction 2.6859 2.8542 -- 146 2961 0.2775 0.3109 -- 100.0
X Ray Diffraction 2.8542 3.0745 -- 160 3002 0.2494 0.342 -- 100.0
X Ray Diffraction 3.0745 3.3838 -- 150 3013 0.2669 0.3148 -- 100.0
X Ray Diffraction 3.3838 3.8731 -- 156 3007 0.2299 0.2458 -- 100.0
X Ray Diffraction 3.8731 4.8787 -- 154 3096 0.1812 0.1885 -- 100.0
X Ray Diffraction 4.8787 43.2459 -- 175 3201 0.2025 0.2395 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 69.4773
Anisotropic B[1][1] 11.4955
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 11.4955
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -25.5966
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 10.999
f_plane_restr 0.002
f_chiral_restr 0.052
f_angle_d 0.724
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2618
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 77

Software

Computing
Computing Package Purpose
CBASS Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
SnB Structure Solution
PHENIX (phenix.refine: dev_1000) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction