X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

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

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 403.06 α = 90
b = 403.06 β = 90
c = 173.45 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
3.54 35 99.2 -- -- -- -- 170381 170381 -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)
3.535 3.68 99.1 -- -- -- -- --

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 3.544 34.742 -- 1.34 170277 170277 8517 99.17 -- 0.1944 0.1925 0.2308 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 3.544 3.5843 -- 294 5219 0.3137 0.3574 -- 98.0
X Ray Diffraction 3.5843 3.6264 -- 272 5342 0.3094 0.3381 -- 99.0
X Ray Diffraction 3.6264 3.6706 -- 288 5324 0.2993 0.3293 -- 99.0
X Ray Diffraction 3.6706 3.717 -- 301 5328 0.2928 0.3265 -- 99.0
X Ray Diffraction 3.717 3.7658 -- 310 5308 0.2705 0.3031 -- 99.0
X Ray Diffraction 3.7658 3.8174 -- 239 5391 0.2709 0.3043 -- 99.0
X Ray Diffraction 3.8174 3.8718 -- 288 5361 0.2592 0.2829 -- 99.0
X Ray Diffraction 3.8718 3.9296 -- 278 5345 0.2542 0.2931 -- 100.0
X Ray Diffraction 3.9296 3.9909 -- 281 5409 0.2425 0.2521 -- 100.0
X Ray Diffraction 3.9909 4.0562 -- 296 5321 0.2378 0.292 -- 100.0
X Ray Diffraction 4.0562 4.126 -- 304 5361 0.2385 0.2658 -- 100.0
X Ray Diffraction 4.126 4.2009 -- 280 5365 0.2209 0.2723 -- 100.0
X Ray Diffraction 4.2009 4.2816 -- 249 5414 0.2227 0.2622 -- 100.0
X Ray Diffraction 4.2816 4.3688 -- 310 5356 0.212 0.2512 -- 100.0
X Ray Diffraction 4.3688 4.4636 -- 308 5385 0.214 0.2493 -- 100.0
X Ray Diffraction 4.4636 4.5673 -- 292 5410 0.1989 0.2301 -- 100.0
X Ray Diffraction 4.5673 4.6812 -- 258 5423 0.1911 0.2228 -- 100.0
X Ray Diffraction 4.6812 4.8075 -- 267 5423 0.194 0.2478 -- 100.0
X Ray Diffraction 4.8075 4.9485 -- 293 5413 0.1844 0.2076 -- 100.0
X Ray Diffraction 4.9485 5.1078 -- 274 5409 0.1832 0.2262 -- 100.0
X Ray Diffraction 5.1078 5.2897 -- 271 5431 0.1775 0.2289 -- 100.0
X Ray Diffraction 5.2897 5.5007 -- 284 5411 0.1693 0.2108 -- 100.0
X Ray Diffraction 5.5007 5.75 -- 287 5430 0.1723 0.2271 -- 100.0
X Ray Diffraction 5.75 6.0517 -- 266 5456 0.175 0.2061 -- 99.0
X Ray Diffraction 6.0517 6.4286 -- 273 5461 0.1756 0.2058 -- 99.0
X Ray Diffraction 6.4286 6.9214 -- 283 5450 0.1684 0.2142 -- 99.0
X Ray Diffraction 6.9214 7.6113 -- 298 5438 0.1604 0.2063 -- 99.0
X Ray Diffraction 7.6113 8.6975 -- 283 5457 0.1569 0.191 -- 98.0
X Ray Diffraction 8.6975 10.9015 -- 281 5466 0.1516 0.1863 -- 97.0
X Ray Diffraction 10.9015 34.7434 -- 309 5453 0.1629 0.2029 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 148.039
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.037
f_plane_restr 0.004
f_dihedral_angle_d 16.781
f_bond_d 0.005
f_angle_d 0.762
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19088
Nucleic Acid Atoms 32506
Heterogen Atoms 283
Solvent Atoms 260

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHENIX refinement version: dev_1555
PDB_EXTRACT data extraction version: 3.11
HKL-2000 data collection
DENZO data reduction
PHENIX phasing