X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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 = 402.52 α = 90
b = 402.52 β = 90
c = 175.89 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 -- 2010-11-07
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
3.39 35 97.5 0.064 -- -- 3.1 192883 192883 -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)
3.386 3.52 98.2 0.647 -- -- 3.0 19239

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 3.386 34.872 -- 1.34 192822 192822 9696 97.01 -- 0.1612 0.159 0.202 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 3.386 3.4246 -- 289 5152 0.2886 0.3161 -- 83.0
X Ray Diffraction 3.4246 3.4649 -- 329 6109 0.2853 0.3308 -- 98.0
X Ray Diffraction 3.4649 3.5071 -- 323 6094 0.2786 0.3538 -- 98.0
X Ray Diffraction 3.5071 3.5514 -- 363 6066 0.2654 0.3063 -- 98.0
X Ray Diffraction 3.5514 3.5981 -- 339 6162 0.2461 0.2959 -- 98.0
X Ray Diffraction 3.5981 3.6474 -- 310 6121 0.234 0.2995 -- 98.0
X Ray Diffraction 3.6474 3.6994 -- 345 6097 0.2187 0.2444 -- 98.0
X Ray Diffraction 3.6994 3.7546 -- 342 6169 0.2062 0.2428 -- 99.0
X Ray Diffraction 3.7546 3.8132 -- 307 6130 0.19 0.2195 -- 98.0
X Ray Diffraction 3.8132 3.8756 -- 309 6158 0.1792 0.2307 -- 98.0
X Ray Diffraction 3.8756 3.9423 -- 340 6150 0.1816 0.2366 -- 99.0
X Ray Diffraction 3.9423 4.0139 -- 308 6180 0.1759 0.2132 -- 99.0
X Ray Diffraction 4.0139 4.091 -- 354 6154 0.1753 0.2307 -- 99.0
X Ray Diffraction 4.091 4.1744 -- 323 6168 0.1569 0.2074 -- 99.0
X Ray Diffraction 4.1744 4.265 -- 308 6204 0.1519 0.2159 -- 99.0
X Ray Diffraction 4.265 4.364 -- 347 6141 0.1443 0.2007 -- 99.0
X Ray Diffraction 4.364 4.473 -- 335 6201 0.1392 0.1805 -- 99.0
X Ray Diffraction 4.473 4.5936 -- 339 6162 0.1333 0.1803 -- 99.0
X Ray Diffraction 4.5936 4.7285 -- 302 6222 0.1311 0.1802 -- 99.0
X Ray Diffraction 4.7285 4.8807 -- 301 6245 0.1289 0.1781 -- 98.0
X Ray Diffraction 4.8807 5.0547 -- 355 6124 0.1259 0.1686 -- 98.0
X Ray Diffraction 5.0547 5.2564 -- 286 6206 0.1189 0.1631 -- 98.0
X Ray Diffraction 5.2564 5.4948 -- 317 6203 0.1222 0.1731 -- 98.0
X Ray Diffraction 5.4948 5.7832 -- 348 6133 0.122 0.177 -- 98.0
X Ray Diffraction 5.7832 6.1437 -- 289 6200 0.1305 0.1807 -- 97.0
X Ray Diffraction 6.1437 6.6151 -- 309 6145 0.1339 0.1729 -- 97.0
X Ray Diffraction 6.6151 7.2754 -- 328 6130 0.1359 0.1906 -- 96.0
X Ray Diffraction 7.2754 8.3156 -- 298 6108 0.1378 0.1799 -- 95.0
X Ray Diffraction 8.3156 10.4301 -- 346 6026 0.1525 0.1745 -- 93.0
X Ray Diffraction 10.4301 34.8735 -- 307 5766 0.1946 0.2146 -- 86.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 141.937
Anisotropic B[1][1] -3.7886
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.7886
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 11.9917
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.067
f_angle_d 0.934
f_bond_d 0.006
f_plane_restr 0.005
f_dihedral_angle_d 18.075
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19088
Nucleic Acid Atoms 32507
Heterogen Atoms 314
Solvent Atoms 538

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: dev_978
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data collection
PHENIX phasing version: dev_978