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 = 403.17 α = 90
b = 403.17 β = 90
c = 173.32 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
3.14 35 99.0 0.069 -- -- 3.4 241842 241842 -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)
3.14 3.25 97.7 0.627 -- -- 3.4 23584

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 3.144 34.647 -- 1.34 241726 241726 12240 98.65 -- 0.1667 0.1646 0.207 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 3.144 3.1798 -- 373 6294 0.2952 0.3293 -- 83.0
X Ray Diffraction 3.1798 3.2171 -- 398 7620 0.2821 0.3168 -- 99.0
X Ray Diffraction 3.2171 3.2563 -- 428 7658 0.2644 0.3029 -- 100.0
X Ray Diffraction 3.2563 3.2975 -- 418 7616 0.2596 0.3026 -- 99.0
X Ray Diffraction 3.2975 3.3409 -- 415 7648 0.2463 0.2938 -- 99.0
X Ray Diffraction 3.3409 3.3866 -- 404 7689 0.2329 0.2883 -- 100.0
X Ray Diffraction 3.3866 3.435 -- 428 7605 0.2316 0.2813 -- 100.0
X Ray Diffraction 3.435 3.4862 -- 436 7631 0.2245 0.2695 -- 100.0
X Ray Diffraction 3.4862 3.5406 -- 421 7707 0.2021 0.2471 -- 100.0
X Ray Diffraction 3.5406 3.5986 -- 418 7651 0.1926 0.2307 -- 100.0
X Ray Diffraction 3.5986 3.6606 -- 404 7660 0.1848 0.2265 -- 100.0
X Ray Diffraction 3.6606 3.7271 -- 419 7668 0.1775 0.2305 -- 100.0
X Ray Diffraction 3.7271 3.7987 -- 424 7677 0.1664 0.2191 -- 100.0
X Ray Diffraction 3.7987 3.8761 -- 379 7735 0.1585 0.1997 -- 100.0
X Ray Diffraction 3.8761 3.9603 -- 404 7682 0.1482 0.1885 -- 100.0
X Ray Diffraction 3.9603 4.0523 -- 420 7690 0.1442 0.1856 -- 100.0
X Ray Diffraction 4.0523 4.1534 -- 420 7714 0.1485 0.1963 -- 100.0
X Ray Diffraction 4.1534 4.2655 -- 372 7739 0.145 0.2016 -- 100.0
X Ray Diffraction 4.2655 4.3908 -- 437 7726 0.1441 0.185 -- 100.0
X Ray Diffraction 4.3908 4.5322 -- 438 7706 0.1429 0.1861 -- 100.0
X Ray Diffraction 4.5322 4.6939 -- 374 7777 0.1397 0.1837 -- 100.0
X Ray Diffraction 4.6939 4.8813 -- 397 7756 0.1328 0.1769 -- 100.0
X Ray Diffraction 4.8813 5.1028 -- 414 7770 0.13 0.1758 -- 100.0
X Ray Diffraction 5.1028 5.3709 -- 381 7761 0.1277 0.1785 -- 100.0
X Ray Diffraction 5.3709 5.706 -- 412 7748 0.137 0.1903 -- 100.0
X Ray Diffraction 5.706 6.1443 -- 386 7824 0.1416 0.2037 -- 99.0
X Ray Diffraction 6.1443 6.7585 -- 413 7758 0.1428 0.1803 -- 99.0
X Ray Diffraction 6.7585 7.727 -- 402 7781 0.1411 0.1866 -- 98.0
X Ray Diffraction 7.727 9.6997 -- 410 7646 0.1584 0.1827 -- 96.0
X Ray Diffraction 9.6997 34.6489 -- 395 7549 0.1858 0.2033 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 122.024
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.022
f_plane_restr 0.006
f_chiral_restr 0.068
f_angle_d 1.212
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19169
Nucleic Acid Atoms 32507
Heterogen Atoms 367
Solvent Atoms 733

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