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 = 402.98 α = 90
b = 402.98 β = 90
c = 172.61 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
3.55 30 96.6 0.156 -- -- 2.8 164584 164584 -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)
3.546 3.68 90.9 0.77 -- -- 2.6 15278

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 3.547 29.752 -- 1.33 164335 164335 8254 96.52 -- 0.1689 0.1661 0.2202 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 3.547 3.5875 -- 269 4746 0.2799 0.3285 -- 89.0
X Ray Diffraction 3.5875 3.6296 -- 266 4839 0.2611 0.2832 -- 91.0
X Ray Diffraction 3.6296 3.6738 -- 259 4871 0.2539 0.3224 -- 92.0
X Ray Diffraction 3.6738 3.7202 -- 274 4961 0.2359 0.3095 -- 93.0
X Ray Diffraction 3.7202 3.769 -- 304 5015 0.223 0.2619 -- 94.0
X Ray Diffraction 3.769 3.8206 -- 228 5094 0.2283 0.2838 -- 95.0
X Ray Diffraction 3.8206 3.875 -- 259 5151 0.2135 0.262 -- 96.0
X Ray Diffraction 3.875 3.9328 -- 257 5162 0.2072 0.2576 -- 97.0
X Ray Diffraction 3.9328 3.9941 -- 281 5196 0.1964 0.2503 -- 97.0
X Ray Diffraction 3.9941 4.0594 -- 289 5239 0.1893 0.2576 -- 98.0
X Ray Diffraction 4.0594 4.1292 -- 312 5226 0.1873 0.2296 -- 99.0
X Ray Diffraction 4.1292 4.2041 -- 259 5318 0.1725 0.2607 -- 99.0
X Ray Diffraction 4.2041 4.2847 -- 261 5309 0.1674 0.2242 -- 99.0
X Ray Diffraction 4.2847 4.3719 -- 299 5247 0.168 0.231 -- 99.0
X Ray Diffraction 4.3719 4.4667 -- 307 5272 0.1591 0.2028 -- 99.0
X Ray Diffraction 4.4667 4.5702 -- 282 5327 0.1489 0.1981 -- 99.0
X Ray Diffraction 4.5702 4.6841 -- 246 5356 0.1447 0.2023 -- 99.0
X Ray Diffraction 4.6841 4.8102 -- 272 5325 0.1434 0.21 -- 99.0
X Ray Diffraction 4.8102 4.9512 -- 290 5309 0.1326 0.1818 -- 99.0
X Ray Diffraction 4.9512 5.1102 -- 269 5326 0.1382 0.2052 -- 99.0
X Ray Diffraction 5.1102 5.2919 -- 274 5318 0.134 0.1983 -- 98.0
X Ray Diffraction 5.2919 5.5025 -- 280 5314 0.1257 0.1806 -- 99.0
X Ray Diffraction 5.5025 5.7512 -- 285 5312 0.1371 0.2103 -- 98.0
X Ray Diffraction 5.7512 6.052 -- 258 5310 0.1424 0.2088 -- 98.0
X Ray Diffraction 6.052 6.4276 -- 271 5315 0.1404 0.1943 -- 98.0
X Ray Diffraction 6.4276 6.9181 -- 272 5303 0.1423 0.2173 -- 97.0
X Ray Diffraction 6.9181 7.6038 -- 289 5245 0.1356 0.2027 -- 96.0
X Ray Diffraction 7.6038 8.6801 -- 271 5262 0.1419 0.1979 -- 96.0
X Ray Diffraction 8.6801 10.8472 -- 280 5262 0.1529 0.1919 -- 95.0
X Ray Diffraction 10.8472 29.7533 -- 291 5151 0.2073 0.2301 -- 90.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 152.503
Anisotropic B[1][1] -17.4238
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -17.4238
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 21.6558
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.822
f_plane_restr 0.009
f_chiral_restr 0.09
f_angle_d 1.598
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 323
Solvent Atoms 382

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