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_dihedral_angle_d 17.614
f_plane_restr 0.005
f_chiral_restr 0.06
f_angle_d 1.034
f_bond_d 0.006
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

Computing
Computing Package Purpose
ADSC Quantum Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK 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
SCALEPACK data reduction
DENZO data collection