X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.7
Temperature 293.0
Details 3% PEG 4000, 4-6% glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 100 mM MES/Imidazole, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 103.62 α = 90
b = 155.13 β = 90
c = 180.41 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2012-04-25
Diffraction Radiation
Monochromator Protocol
LN2 cooled fixed-exit Si(111) monochromator, Sagittally - horizontally focussed SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.00001 SLS X06SA

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
2.3 77.6 99.9 0.133 -- -- 13.6 129393 129393 0.0 0.0 50.3
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)
2.3 2.36 100.0 -- -- 1.17 13.8 9467

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 2.3 77.565 -- 1.99 129393 129379 6505 99.99 0.1935 0.1935 0.1907 0.2463 --
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 2.3 2.3261 -- 197 4010 0.3477 0.4087 -- 100.0
X Ray Diffraction 2.3261 2.3535 -- 239 4090 0.3172 0.3742 -- 100.0
X Ray Diffraction 2.3535 2.3822 -- 241 3984 0.2973 0.3511 -- 100.0
X Ray Diffraction 2.3822 2.4123 -- 194 4091 0.2856 0.3264 -- 100.0
X Ray Diffraction 2.4123 2.4441 -- 236 4016 0.28 0.3501 -- 100.0
X Ray Diffraction 2.4441 2.4775 -- 209 4089 0.283 0.3551 -- 100.0
X Ray Diffraction 2.4775 2.5129 -- 215 4042 0.2685 0.3279 -- 100.0
X Ray Diffraction 2.5129 2.5505 -- 205 4059 0.2642 0.3275 -- 100.0
X Ray Diffraction 2.5505 2.5903 -- 198 4138 0.242 0.325 -- 100.0
X Ray Diffraction 2.5903 2.6328 -- 219 3985 0.243 0.3175 -- 100.0
X Ray Diffraction 2.6328 2.6782 -- 205 4102 0.2484 0.3042 -- 100.0
X Ray Diffraction 2.6782 2.7269 -- 211 4096 0.2408 0.3087 -- 100.0
X Ray Diffraction 2.7269 2.7793 -- 213 4028 0.2252 0.2995 -- 100.0
X Ray Diffraction 2.7793 2.8361 -- 238 4036 0.2175 0.32 -- 100.0
X Ray Diffraction 2.8361 2.8977 -- 232 4096 0.2072 0.2747 -- 100.0
X Ray Diffraction 2.8977 2.9651 -- 223 4062 0.2079 0.2755 -- 100.0
X Ray Diffraction 2.9651 3.0393 -- 225 4050 0.1997 0.2532 -- 100.0
X Ray Diffraction 3.0393 3.1215 -- 216 4093 0.1982 0.2833 -- 100.0
X Ray Diffraction 3.1215 3.2133 -- 215 4091 0.2054 0.2887 -- 100.0
X Ray Diffraction 3.2133 3.317 -- 189 4115 0.2037 0.2774 -- 100.0
X Ray Diffraction 3.317 3.4356 -- 213 4092 0.1937 0.2455 -- 100.0
X Ray Diffraction 3.4356 3.5732 -- 197 4127 0.1818 0.2447 -- 100.0
X Ray Diffraction 3.5732 3.7358 -- 219 4090 0.1802 0.2287 -- 100.0
X Ray Diffraction 3.7358 3.9327 -- 205 4124 0.1703 0.2377 -- 100.0
X Ray Diffraction 3.9327 4.1791 -- 219 4136 0.1579 0.2121 -- 100.0
X Ray Diffraction 4.1791 4.5017 -- 247 4108 0.1435 0.1973 -- 100.0
X Ray Diffraction 4.5017 4.9547 -- 215 4157 0.1336 0.1814 -- 100.0
X Ray Diffraction 4.9547 5.6715 -- 216 4169 0.1688 0.2172 -- 100.0
X Ray Diffraction 5.6715 7.1447 -- 225 4211 0.1933 0.262 -- 100.0
X Ray Diffraction 7.1447 77.6091 -- 229 4387 0.1792 0.1924 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.6336
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 11.8387
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.8897
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.051
f_dihedral_angle_d 15.184
f_angle_d 0.943
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 17039
Nucleic Acid Atoms 0
Heterogen Atoms 240
Solvent Atoms 306

Software

Computing
Computing Package Purpose
REMDAQ Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHASER model building
REMDAQ data collection