X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Hanging Drop
pH 6.5
Temperature 277.0
Details MPD, pH 6.5, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 404.04 α = 90
b = 404.04 β = 90
c = 173.53 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-11-07
Diffraction Radiation
Monochromator Protocol
Kohzu HLD8-24 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.98 APS 24-ID-C

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
3.35 35 98.3 0.062 -- -- 3.3 200934 200934 -3.0 -3.0 --
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)
3.348 3.47 99.0 0.634 -- -- 3.3 19994

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 3.348 34.552 -- 1.34 200881 200881 10115 98.32 -- 0.1695 0.1676 0.2063 FROM PDB ENTRY 2VQE
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 3.348 3.3864 -- 330 6238 0.2899 0.3452 -- 98.0
X Ray Diffraction 3.3864 3.4262 -- 360 6294 0.2866 0.35 -- 99.0
X Ray Diffraction 3.4262 3.4679 -- 340 6342 0.2692 0.3022 -- 99.0
X Ray Diffraction 3.4679 3.5118 -- 371 6352 0.2569 0.3028 -- 100.0
X Ray Diffraction 3.5118 3.558 -- 337 6334 0.2442 0.2795 -- 99.0
X Ray Diffraction 3.558 3.6066 -- 353 6342 0.2304 0.2666 -- 99.0
X Ray Diffraction 3.6066 3.6581 -- 343 6363 0.2188 0.2532 -- 99.0
X Ray Diffraction 3.6581 3.7127 -- 350 6341 0.2113 0.2605 -- 99.0
X Ray Diffraction 3.7127 3.7706 -- 363 6340 0.1971 0.2287 -- 99.0
X Ray Diffraction 3.7706 3.8323 -- 292 6445 0.1953 0.2412 -- 100.0
X Ray Diffraction 3.8323 3.8983 -- 338 6370 0.1832 0.2114 -- 99.0
X Ray Diffraction 3.8983 3.9691 -- 337 6359 0.1728 0.2106 -- 99.0
X Ray Diffraction 3.9691 4.0454 -- 348 6362 0.1689 0.2102 -- 99.0
X Ray Diffraction 4.0454 4.1278 -- 369 6386 0.17 0.216 -- 99.0
X Ray Diffraction 4.1278 4.2174 -- 321 6408 0.1547 0.1972 -- 100.0
X Ray Diffraction 4.2174 4.3153 -- 328 6423 0.1551 0.223 -- 99.0
X Ray Diffraction 4.3153 4.423 -- 346 6387 0.1568 0.195 -- 99.0
X Ray Diffraction 4.423 4.5424 -- 369 6395 0.1495 0.1868 -- 99.0
X Ray Diffraction 4.5424 4.6757 -- 326 6445 0.1448 0.1883 -- 99.0
X Ray Diffraction 4.6757 4.8263 -- 302 6402 0.1379 0.1633 -- 99.0
X Ray Diffraction 4.8263 4.9983 -- 353 6406 0.129 0.174 -- 99.0
X Ray Diffraction 4.9983 5.1978 -- 316 6444 0.1335 0.1826 -- 99.0
X Ray Diffraction 5.1978 5.4334 -- 323 6442 0.1346 0.1853 -- 99.0
X Ray Diffraction 5.4334 5.7187 -- 341 6380 0.1325 0.1727 -- 99.0
X Ray Diffraction 5.7187 6.0752 -- 326 6405 0.1415 0.1871 -- 98.0
X Ray Diffraction 6.0752 6.5413 -- 307 6411 0.148 0.181 -- 98.0
X Ray Diffraction 6.5413 7.1943 -- 341 6398 0.1441 0.1943 -- 97.0
X Ray Diffraction 7.1943 8.223 -- 315 6347 0.1451 0.1985 -- 96.0
X Ray Diffraction 8.223 10.3142 -- 359 6260 0.163 0.1857 -- 94.0
X Ray Diffraction 10.3142 34.5537 -- 311 5945 0.2039 0.2145 -- 86.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 147.169
Anisotropic B[1][1] -8.699
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -8.699
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 17.398
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.902
f_plane_restr 0.005
f_chiral_restr 0.068
f_angle_d 0.964
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19088
Nucleic Acid Atoms 32507
Heterogen Atoms 306
Solvent Atoms 263

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX (phenix.refine: dev_978) Structure Solution
PHENIX (phenix.refine: dev_978) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
SCALEPACK data reduction
DENZO data collection