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_plane_restr 0.006
f_dihedral_angle_d 18.022
f_bond_d 0.007
f_angle_d 1.212
f_chiral_restr 0.068
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

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