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_angle_d 1.973
f_dihedral_angle_d 19.943
f_chiral_restr 0.094
f_plane_restr 0.009
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

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement version: dev_1119
PDB_EXTRACT data extraction version: 3.11
CBASS data collection
PHENIX phasing version: dev_1119