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 = 65.28 α = 90
b = 79.02 β = 99.87
c = 69.7 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
1.4 26.67 99.6 -- 0.044 -- 3.73 136423 136423 -3.0 -3.0 13.4
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)
1.4 1.44 99.7 -- 0.71 2.39 3.67 36943

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 1.4 26.674 -- 0.0 136413 136413 6924 99.6 0.1654 0.1654 0.1648 0.1779 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 1.4 1.4159 4274 244 4274 0.2646 0.2781 -- 100.0
X Ray Diffraction 1.4159 1.4326 4293 248 4293 0.2595 0.2962 -- 100.0
X Ray Diffraction 1.4326 1.45 4340 224 4340 0.2464 0.2683 -- 100.0
X Ray Diffraction 1.45 1.4684 4246 235 4246 0.2345 0.2744 -- 100.0
X Ray Diffraction 1.4684 1.4877 4357 239 4357 0.2294 0.2578 -- 100.0
X Ray Diffraction 1.4877 1.5081 4272 253 4272 0.2155 0.2435 -- 100.0
X Ray Diffraction 1.5081 1.5296 4304 234 4304 0.2088 0.217 -- 100.0
X Ray Diffraction 1.5296 1.5525 4338 226 4338 0.2064 0.222 -- 100.0
X Ray Diffraction 1.5525 1.5767 4294 215 4294 0.1938 0.2192 -- 100.0
X Ray Diffraction 1.5767 1.6026 4304 231 4304 0.1873 0.2123 -- 100.0
X Ray Diffraction 1.6026 1.6302 4305 239 4305 0.1856 0.2262 -- 100.0
X Ray Diffraction 1.6302 1.6598 4296 238 4296 0.1773 0.1906 -- 100.0
X Ray Diffraction 1.6598 1.6918 4289 246 4289 0.1717 0.2029 -- 100.0
X Ray Diffraction 1.6918 1.7263 4358 208 4358 0.1705 0.1817 -- 100.0
X Ray Diffraction 1.7263 1.7638 4344 213 4344 0.1602 0.1702 -- 100.0
X Ray Diffraction 1.7638 1.8048 4311 236 4311 0.1532 0.1931 -- 100.0
X Ray Diffraction 1.8048 1.85 4297 233 4297 0.1513 0.1678 -- 100.0
X Ray Diffraction 1.85 1.9 4304 230 4304 0.1554 0.154 -- 100.0
X Ray Diffraction 1.9 1.9558 4307 248 4307 0.1548 0.1735 -- 100.0
X Ray Diffraction 1.9558 2.019 4316 221 4316 0.1521 0.1728 -- 100.0
X Ray Diffraction 2.019 2.0911 4336 212 4336 0.149 0.1531 -- 99.0
X Ray Diffraction 2.0911 2.1748 4356 220 4356 0.1537 0.1636 -- 100.0
X Ray Diffraction 2.1748 2.2737 4276 233 4276 0.1568 0.1614 -- 99.0
X Ray Diffraction 2.2737 2.3935 4279 270 4279 0.1513 0.1645 -- 99.0
X Ray Diffraction 2.3935 2.5434 4296 219 4296 0.1529 0.167 -- 99.0
X Ray Diffraction 2.5434 2.7396 4317 215 4317 0.159 0.182 -- 99.0
X Ray Diffraction 2.7396 3.0149 4348 219 4348 0.1623 0.1729 -- 99.0
X Ray Diffraction 3.0149 3.4504 4348 211 4348 0.1553 0.1634 -- 99.0
X Ray Diffraction 3.4504 4.3441 4353 250 4353 0.1446 0.1433 -- 99.0
X Ray Diffraction 4.3441 26.6792 4431 214 4431 0.1596 0.1685 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic, TLS
Mean Isotropic B 21.68
Anisotropic B[1][1] -1.6254
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.5603
Anisotropic B[2][2] -1.2109
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.8362
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.074
f_dihedral_angle_d 11.765
f_angle_d 1.062
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4793
Nucleic Acid Atoms 0
Heterogen Atoms 96
Solvent Atoms 967

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