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 = 402.98 α = 90
b = 402.98 β = 90
c = 173.12 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 Monochromator 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
3.35 35 88.2 0.072 -- -- 4.4 178536 178536 -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)
3.35 3.47 92.3 0.624 -- -- 4.3 18472

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 3.35 34.002 -- 1.33 178313 178313 8991 87.75 -- 0.1701 0.1677 0.2152 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 3.3461 3.3841 -- 278 5150 0.2853 0.3387 -- 81.0
X Ray Diffraction 3.3841 3.4239 -- 346 5851 0.2716 0.334 -- 92.0
X Ray Diffraction 3.4239 3.4656 -- 324 5831 0.2631 0.2976 -- 92.0
X Ray Diffraction 3.4656 3.5095 -- 340 5830 0.2483 0.2974 -- 92.0
X Ray Diffraction 3.5095 3.5556 -- 324 5799 0.2403 0.2823 -- 92.0
X Ray Diffraction 3.5556 3.6042 -- 318 5852 0.226 0.2436 -- 92.0
X Ray Diffraction 3.6042 3.6557 -- 301 5822 0.2218 0.2686 -- 91.0
X Ray Diffraction 3.6557 3.7102 -- 317 5772 0.2191 0.2861 -- 91.0
X Ray Diffraction 3.7102 3.7681 -- 330 5796 0.2078 0.2584 -- 91.0
X Ray Diffraction 3.7681 3.8298 -- 269 5795 0.2012 0.2789 -- 91.0
X Ray Diffraction 3.8298 3.8957 -- 294 5772 0.1944 0.2209 -- 90.0
X Ray Diffraction 3.8957 3.9665 -- 308 5751 0.1758 0.2352 -- 90.0
X Ray Diffraction 3.9665 4.0426 -- 321 5734 0.1722 0.2297 -- 90.0
X Ray Diffraction 4.0426 4.125 -- 322 5717 0.1683 0.2166 -- 90.0
X Ray Diffraction 4.125 4.2145 -- 275 5749 0.1637 0.2293 -- 89.0
X Ray Diffraction 4.2145 4.3124 -- 292 5683 0.1624 0.2311 -- 89.0
X Ray Diffraction 4.3124 4.42 -- 297 5708 0.1651 0.2061 -- 89.0
X Ray Diffraction 4.42 4.5393 -- 336 5644 0.1578 0.2179 -- 89.0
X Ray Diffraction 4.5393 4.6725 -- 284 5674 0.1507 0.1927 -- 88.0
X Ray Diffraction 4.6725 4.8229 -- 270 5684 0.1424 0.1844 -- 88.0
X Ray Diffraction 4.8229 4.9948 -- 311 5576 0.1349 0.2042 -- 87.0
X Ray Diffraction 4.9948 5.1941 -- 264 5599 0.1341 0.1737 -- 87.0
X Ray Diffraction 5.1941 5.4296 -- 281 5611 0.1353 0.208 -- 86.0
X Ray Diffraction 5.4296 5.7146 -- 308 5535 0.1427 0.2038 -- 86.0
X Ray Diffraction 5.7146 6.0707 -- 266 5536 0.1438 0.1951 -- 85.0
X Ray Diffraction 6.0707 6.5364 -- 277 5485 0.1472 0.1951 -- 84.0
X Ray Diffraction 6.5364 7.1886 -- 294 5464 0.1358 0.1757 -- 84.0
X Ray Diffraction 7.1886 8.2159 -- 270 5415 0.1417 0.2017 -- 83.0
X Ray Diffraction 8.2159 10.3032 -- 302 5322 0.1584 0.1891 -- 81.0
X Ray Diffraction 10.3032 34.0035 -- 272 5165 0.1877 0.205 -- 75.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 144.32
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.034
f_bond_d 0.006
f_chiral_restr 0.06
f_plane_restr 0.005
f_dihedral_angle_d 17.614
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19093
Nucleic Acid Atoms 32487
Heterogen Atoms 288
Solvent Atoms 233

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: dev_1119
PDB_EXTRACT data extraction version: 3.11
ADSC data collection version: Quantum
PHENIX phasing version: dev_1119