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 = 399.62 α = 90
b = 399.62 β = 90
c = 216.07 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
PIXEL DECTRIS PILATUS 6M -- 2012-03-01
Diffraction Radiation
Monochromator Protocol
Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 0.98 NSLS X25

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
3.85 50 99.3 0.117 -- -- -- 163037 163037 -3.0 -3.0 144.028
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)
3.85 3.95 99.9 0.011 -- 1.9 -- --

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 3.85 47.286 -- 1.99 162952 162952 8210 99.27 -- 0.1553 0.1528 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 3.85 3.8937 -- 304 5050 0.2588 0.3377 -- 100.0
X Ray Diffraction 3.8937 3.9395 -- 283 5137 0.232 0.2945 -- 100.0
X Ray Diffraction 3.9395 3.9875 -- 278 5147 0.232 0.2858 -- 100.0
X Ray Diffraction 3.9875 4.038 -- 275 5124 0.2159 0.2814 -- 100.0
X Ray Diffraction 4.038 4.0911 -- 263 5142 0.2065 0.2765 -- 100.0
X Ray Diffraction 4.0911 4.1471 -- 288 5116 0.2011 0.2486 -- 100.0
X Ray Diffraction 4.1471 4.2063 -- 279 5156 0.1819 0.2271 -- 100.0
X Ray Diffraction 4.2063 4.269 -- 240 5146 0.1751 0.2289 -- 100.0
X Ray Diffraction 4.269 4.3357 -- 270 5166 0.1671 0.2234 -- 100.0
X Ray Diffraction 4.3357 4.4067 -- 282 5115 0.1631 0.2079 -- 100.0
X Ray Diffraction 4.4067 4.4827 -- 257 5163 0.1634 0.2205 -- 100.0
X Ray Diffraction 4.4827 4.5641 -- 229 5171 0.1568 0.2202 -- 100.0
X Ray Diffraction 4.5641 4.6518 -- 271 5143 0.1508 0.2095 -- 100.0
X Ray Diffraction 4.6518 4.7467 -- 291 5126 0.1429 0.1988 -- 100.0
X Ray Diffraction 4.7467 4.8498 -- 260 5133 0.1321 0.1938 -- 100.0
X Ray Diffraction 4.8498 4.9625 -- 252 5186 0.1386 0.196 -- 100.0
X Ray Diffraction 4.9625 5.0865 -- 266 5180 0.1314 0.1809 -- 100.0
X Ray Diffraction 5.0865 5.2238 -- 285 5149 0.1239 0.1809 -- 100.0
X Ray Diffraction 5.2238 5.3773 -- 275 5146 0.1215 0.1662 -- 100.0
X Ray Diffraction 5.3773 5.5506 -- 282 5165 0.1171 0.1767 -- 99.0
X Ray Diffraction 5.5506 5.7487 -- 250 5151 0.1163 0.1685 -- 99.0
X Ray Diffraction 5.7487 5.9784 -- 254 5196 0.1162 0.1738 -- 99.0
X Ray Diffraction 5.9784 6.2499 -- 286 5125 0.1173 0.1728 -- 99.0
X Ray Diffraction 6.2499 6.5786 -- 287 5166 0.1206 0.1789 -- 99.0
X Ray Diffraction 6.5786 6.9896 -- 269 5190 0.1172 0.1676 -- 99.0
X Ray Diffraction 6.9896 7.5273 -- 275 5162 0.1195 0.1615 -- 99.0
X Ray Diffraction 7.5273 8.2811 -- 287 5197 0.1268 0.1799 -- 99.0
X Ray Diffraction 8.2811 9.4711 -- 279 5192 0.1479 0.1965 -- 98.0
X Ray Diffraction 9.4711 11.901 -- 296 5190 0.1475 0.1903 -- 98.0
X Ray Diffraction 11.901 47.2898 -- 297 5312 0.214 0.2385 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 162.958
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.943
f_plane_restr 0.009
f_chiral_restr 0.094
f_angle_d 1.973
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19088
Nucleic Acid Atoms 32550
Heterogen Atoms 174
Solvent Atoms 279

Software

Computing
Computing Package Purpose
CBASS Data Collection
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX (phenix.refine: dev_1119) Structure Solution
PHENIX (phenix.refine: dev_1119) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction