X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 291.0
Details 0.1M HEPES, 8% 2-methyl-2,4-pentadediol, 13% PEG 6000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.91 α = 90
b = 151.82 β = 90
c = 181.58 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
CCD ADSC QUANTUM 315r -- 2008-12-13
Diffraction Radiation
Monochromator Protocol
Si(311) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 0.98 SSRL BL7-1

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
3.2 48.75 99.0 0.144 0.144 -- 4.1 -- 73790 1.0 1.0 50.19
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)
3.2 3.28 99.5 0.506 0.506 1.4 4.1 2903

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 3.2 48.747 -- 0.03 -- 68907 3452 90.03 -- 0.239 0.237 0.27 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 3.2 3.244 -- 107 2368 0.31 0.329 -- 81.0
X Ray Diffraction 3.244 3.29 -- 136 2426 0.292 0.331 -- 84.0
X Ray Diffraction 3.29 3.339 -- 137 2451 0.287 0.327 -- 84.0
X Ray Diffraction 3.339 3.391 -- 139 2436 0.299 0.334 -- 85.0
X Ray Diffraction 3.391 3.447 -- 119 2423 0.352 0.381 -- 82.0
X Ray Diffraction 3.447 3.507 -- 143 2373 0.297 0.354 -- 83.0
X Ray Diffraction 3.507 3.57 -- 146 2559 0.248 0.289 -- 89.0
X Ray Diffraction 3.57 3.639 -- 141 2573 0.263 0.306 -- 88.0
X Ray Diffraction 3.639 3.713 -- 146 2485 0.295 0.338 -- 86.0
X Ray Diffraction 3.713 3.794 -- 151 2633 0.255 0.293 -- 91.0
X Ray Diffraction 3.794 3.882 -- 145 2552 0.26 0.318 -- 89.0
X Ray Diffraction 3.882 3.979 -- 126 2555 0.288 0.38 -- 87.0
X Ray Diffraction 3.979 4.087 -- 121 2755 0.228 0.274 -- 94.0
X Ray Diffraction 4.087 4.207 -- 163 2688 0.207 0.261 -- 93.0
X Ray Diffraction 4.207 4.343 -- 119 2795 0.197 0.21 -- 94.0
X Ray Diffraction 4.343 4.498 -- 122 2753 0.186 0.214 -- 95.0
X Ray Diffraction 4.498 4.677 -- 148 2717 0.17 0.18 -- 94.0
X Ray Diffraction 4.677 4.89 -- 130 2756 0.178 0.181 -- 94.0
X Ray Diffraction 4.89 5.148 -- 152 2724 0.193 0.216 -- 93.0
X Ray Diffraction 5.148 5.47 -- 124 2739 0.21 0.245 -- 94.0
X Ray Diffraction 5.47 5.892 -- 157 2674 0.221 0.251 -- 93.0
X Ray Diffraction 5.892 6.483 -- 126 2745 0.219 0.273 -- 94.0
X Ray Diffraction 6.483 7.419 -- 143 2751 0.209 0.2 -- 94.0
X Ray Diffraction 7.419 9.336 -- 182 2746 0.173 0.207 -- 96.0
X Ray Diffraction 9.336 48.753 -- 129 2778 0.189 0.197 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 44.89
Anisotropic B[1][1] 16.201
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.201
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -9.999
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.296
f_plane_restr 0.009
f_chiral_restr 0.084
f_angle_d 1.467
f_bond_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13435
Nucleic Acid Atoms 0
Heterogen Atoms 244
Solvent Atoms 34

Software

Computing
Computing Package Purpose
BlueIce Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASES Structure Solution
PHENIX (phenix.refine) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine) refinement
PHASES model building
BlueIce data collection