X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 0.1 M Imidazole, 8.25% (w/v) PEG 8000, 1% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.23 α = 90
b = 79.03 β = 99.84
c = 69.64 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2010-08-08
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM

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
1.28 29.04 99.8 -- 0.041 -- 3.7 -- 178400 0.0 -3.0 12.1
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)
1.28 1.31 99.8 -- 0.725 2.14 3.6 13137

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
MOLECULAR REPLACEMENT 1.28 29.038 -- 0.0 178400 178393 8988 99.83 -- 0.1675 0.1667 0.1814 RANDOM
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 1.28 1.2945 5537 332 5537 0.2791 0.2814 -- 100.0
X Ray Diffraction 1.2945 1.3098 5662 278 5662 0.2603 0.2613 -- 100.0
X Ray Diffraction 1.3098 1.3257 5634 287 5634 0.2565 0.2767 -- 100.0
X Ray Diffraction 1.3257 1.3425 5639 292 5639 0.2479 0.2825 -- 100.0
X Ray Diffraction 1.3425 1.3602 5671 279 5671 0.2423 0.2331 -- 100.0
X Ray Diffraction 1.3602 1.3788 5598 301 5598 0.2281 0.2522 -- 100.0
X Ray Diffraction 1.3788 1.3985 5679 280 5679 0.2173 0.2232 -- 100.0
X Ray Diffraction 1.3985 1.4194 5615 316 5615 0.2119 0.2262 -- 100.0
X Ray Diffraction 1.4194 1.4416 5629 303 5629 0.2058 0.2413 -- 100.0
X Ray Diffraction 1.4416 1.4652 5628 308 5628 0.1908 0.2171 -- 100.0
X Ray Diffraction 1.4652 1.4905 5616 314 5616 0.1895 0.2028 -- 100.0
X Ray Diffraction 1.4905 1.5176 5627 319 5627 0.183 0.1981 -- 100.0
X Ray Diffraction 1.5176 1.5468 5646 303 5646 0.1766 0.2087 -- 100.0
X Ray Diffraction 1.5468 1.5783 5621 286 5621 0.1695 0.1922 -- 100.0
X Ray Diffraction 1.5783 1.6126 5646 308 5646 0.1624 0.1867 -- 100.0
X Ray Diffraction 1.6126 1.6502 5644 307 5644 0.1644 0.1972 -- 100.0
X Ray Diffraction 1.6502 1.6914 5603 322 5603 0.1597 0.1727 -- 100.0
X Ray Diffraction 1.6914 1.7371 5692 272 5692 0.1544 0.174 -- 100.0
X Ray Diffraction 1.7371 1.7883 5632 296 5632 0.1485 0.166 -- 100.0
X Ray Diffraction 1.7883 1.846 5643 302 5643 0.1409 0.1563 -- 100.0
X Ray Diffraction 1.846 1.9119 5640 303 5640 0.1489 0.1591 -- 100.0
X Ray Diffraction 1.9119 1.9885 5675 320 5675 0.1481 0.1619 -- 100.0
X Ray Diffraction 1.9885 2.0789 5637 280 5637 0.1479 0.1539 -- 100.0
X Ray Diffraction 2.0789 2.1885 5666 284 5666 0.1521 0.1581 -- 100.0
X Ray Diffraction 2.1885 2.3256 5671 321 5671 0.1552 0.1606 -- 100.0
X Ray Diffraction 2.3256 2.505 5642 317 5642 0.1552 0.1706 -- 100.0
X Ray Diffraction 2.505 2.757 5658 287 5658 0.1642 0.1784 -- 100.0
X Ray Diffraction 2.757 3.1555 5698 286 5698 0.1701 0.1864 -- 100.0
X Ray Diffraction 3.1555 3.974 5692 296 5692 0.1569 0.1783 -- 100.0
X Ray Diffraction 3.974 29.0453 5764 289 5764 0.1533 0.1625 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic, TLS
Mean Isotropic B 21.433
Anisotropic B[1][1] -0.8882
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.8004
Anisotropic B[2][2] -0.6755
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.5637
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_chiral_restr 0.095
f_dihedral_angle_d 13.683
f_angle_d 1.357
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4829
Nucleic Acid Atoms 0
Heterogen Atoms 139
Solvent Atoms 825

Software

Computing
Computing Package Purpose
SERGUI Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER (2.1.4) Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
PHASER version: (2.1.4) model building
SERGUI data collection