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 = 403.74 α = 90
b = 403.74 β = 90
c = 173.22 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 -- 2010-04-19
Diffraction Radiation
Monochromator Protocol
single crystal Si(220) side-bounce SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.98 APS 24-ID-E

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
3.65 30 97.2 0.12 -- -- 3.1 153457 153457 -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)
3.646 3.78 97.5 0.759 -- -- 3.1 15255

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 3.646 29.771 -- 1.34 153299 153299 7637 96.99 -- 0.1675 0.1645 0.223 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 3.646 3.6876 -- 257 4479 0.2994 0.336 -- 90.0
X Ray Diffraction 3.6876 3.7309 -- 247 4830 0.2725 0.3356 -- 98.0
X Ray Diffraction 3.7309 3.7763 -- 287 4822 0.2521 0.3128 -- 98.0
X Ray Diffraction 3.7763 3.824 -- 214 4906 0.2504 0.3082 -- 98.0
X Ray Diffraction 3.824 3.8743 -- 270 4883 0.2299 0.2777 -- 99.0
X Ray Diffraction 3.8743 3.9272 -- 247 4900 0.2296 0.281 -- 99.0
X Ray Diffraction 3.9272 3.9832 -- 249 4862 0.2178 0.2863 -- 99.0
X Ray Diffraction 3.9832 4.0425 -- 277 4895 0.2102 0.253 -- 99.0
X Ray Diffraction 4.0425 4.1055 -- 295 4880 0.2 0.2611 -- 99.0
X Ray Diffraction 4.1055 4.1727 -- 233 4940 0.1925 0.2626 -- 99.0
X Ray Diffraction 4.1727 4.2444 -- 239 4926 0.181 0.2615 -- 99.0
X Ray Diffraction 4.2444 4.3214 -- 276 4914 0.1719 0.2346 -- 99.0
X Ray Diffraction 4.3214 4.4042 -- 256 4907 0.1715 0.2337 -- 99.0
X Ray Diffraction 4.4042 4.4938 -- 294 4872 0.1678 0.2254 -- 99.0
X Ray Diffraction 4.4938 4.5912 -- 249 4930 0.1583 0.2091 -- 99.0
X Ray Diffraction 4.5912 4.6976 -- 230 4945 0.1535 0.1948 -- 99.0
X Ray Diffraction 4.6976 4.8146 -- 253 4913 0.1464 0.2108 -- 99.0
X Ray Diffraction 4.8146 4.9442 -- 262 4894 0.1369 0.2025 -- 98.0
X Ray Diffraction 4.9442 5.089 -- 258 4905 0.1416 0.2058 -- 98.0
X Ray Diffraction 5.089 5.2524 -- 226 4938 0.1352 0.2083 -- 98.0
X Ray Diffraction 5.2524 5.439 -- 253 4887 0.1253 0.1891 -- 98.0
X Ray Diffraction 5.439 5.6554 -- 261 4840 0.1268 0.1959 -- 97.0
X Ray Diffraction 5.6554 5.9109 -- 250 4860 0.131 0.1911 -- 97.0
X Ray Diffraction 5.9109 6.2198 -- 243 4824 0.142 0.2267 -- 96.0
X Ray Diffraction 6.2198 6.6055 -- 251 4869 0.139 0.1991 -- 97.0
X Ray Diffraction 6.6055 7.1091 -- 250 4870 0.1313 0.1925 -- 96.0
X Ray Diffraction 7.1091 7.8128 -- 248 4824 0.1236 0.1919 -- 95.0
X Ray Diffraction 7.8128 8.9167 -- 259 4778 0.1345 0.188 -- 94.0
X Ray Diffraction 8.9167 11.1354 -- 249 4783 0.1459 0.2006 -- 93.0
X Ray Diffraction 11.1354 29.7716 -- 254 4586 0.2123 0.2462 -- 86.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 173.946
Anisotropic B[1][1] -9.8508
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -9.8508
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 16.0687
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.336
f_plane_restr 0.009
f_chiral_restr 0.089
f_angle_d 1.59
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19088
Nucleic Acid Atoms 32509
Heterogen Atoms 291
Solvent Atoms 416

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