X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop
pH 6.5
Temperature 277.0
Details MPD, pH 6.5, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 402.45 α = 90
b = 402.45 β = 90
c = 176.92 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
3.15 35 98.3 0.078 -- -- 3.3 243896 243896 -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)
3.1484 3.26 99.1 0.677 -- -- 3.3 24313

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 3.1484 34.615 -- 1.34 243798 243798 12361 98.24 0.1701 0.1701 0.1682 0.2054 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 3.1484 3.1841 -- 454 7625 0.3005 0.3471 -- 98.0
X Ray Diffraction 3.1841 3.2216 -- 428 7660 0.2854 0.3134 -- 98.0
X Ray Diffraction 3.2216 3.2608 -- 411 7684 0.2654 0.2934 -- 99.0
X Ray Diffraction 3.2608 3.3021 -- 431 7689 0.2588 0.298 -- 99.0
X Ray Diffraction 3.3021 3.3455 -- 415 7717 0.2416 0.2601 -- 99.0
X Ray Diffraction 3.3455 3.3913 -- 399 7753 0.232 0.2709 -- 99.0
X Ray Diffraction 3.3913 3.4397 -- 423 7711 0.223 0.2595 -- 99.0
X Ray Diffraction 3.4397 3.491 -- 438 7694 0.2186 0.253 -- 99.0
X Ray Diffraction 3.491 3.5455 -- 422 7697 0.204 0.2422 -- 99.0
X Ray Diffraction 3.5455 3.6036 -- 439 7716 0.187 0.2189 -- 99.0
X Ray Diffraction 3.6036 3.6656 -- 397 7760 0.1792 0.217 -- 100.0
X Ray Diffraction 3.6656 3.7322 -- 453 7669 0.1765 0.2047 -- 99.0
X Ray Diffraction 3.7322 3.8039 -- 403 7737 0.1661 0.215 -- 99.0
X Ray Diffraction 3.8039 3.8815 -- 380 7775 0.1588 0.1982 -- 99.0
X Ray Diffraction 3.8815 3.9657 -- 412 7770 0.1533 0.2017 -- 99.0
X Ray Diffraction 3.9657 4.0578 -- 418 7746 0.1508 0.184 -- 99.0
X Ray Diffraction 4.0578 4.1592 -- 424 7730 0.1452 0.183 -- 99.0
X Ray Diffraction 4.1592 4.2714 -- 395 7786 0.1396 0.1869 -- 99.0
X Ray Diffraction 4.2714 4.3969 -- 437 7743 0.1399 0.1877 -- 99.0
X Ray Diffraction 4.3969 4.5385 -- 431 7734 0.1367 0.1677 -- 99.0
X Ray Diffraction 4.5385 4.7003 -- 384 7806 0.1354 0.1781 -- 99.0
X Ray Diffraction 4.7003 4.888 -- 374 7829 0.1346 0.1723 -- 99.0
X Ray Diffraction 4.888 5.1098 -- 427 7737 0.1282 0.173 -- 99.0
X Ray Diffraction 5.1098 5.3783 -- 391 7769 0.1307 0.1717 -- 98.0
X Ray Diffraction 5.3783 5.7139 -- 411 7756 0.1335 0.1828 -- 98.0
X Ray Diffraction 5.7139 6.1528 -- 382 7759 0.1412 0.1724 -- 98.0
X Ray Diffraction 6.1528 6.7678 -- 402 7740 0.1421 0.1875 -- 97.0
X Ray Diffraction 6.7678 7.7375 -- 390 7687 0.1496 0.1805 -- 96.0
X Ray Diffraction 7.7375 9.7127 -- 413 7578 0.1733 0.1988 -- 94.0
X Ray Diffraction 9.7127 34.6167 -- 377 7380 0.218 0.243 -- 88.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 105.725
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.596
f_plane_restr 0.004
f_chiral_restr 0.049
f_angle_d 0.816
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19134
Nucleic Acid Atoms 32460
Heterogen Atoms 602
Solvent Atoms 24

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX 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