X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 50 mM PIPES, 100 mM MgCl2 [pH 7.0], and 10-15% PEG-8000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 218.48 α = 90
b = 106.15 β = 90.39
c = 282.23 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F -- 2014-10-27
Diffraction Radiation
Monochromator Protocol
Cryo-Cooled double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 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
3.6 59.45 95.0 -- 0.134 5.2 2.7 -- 142673 -- -- 81.4
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)
3.6 3.79 96.7 0.65 0.65 1.2 2.7 --

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 3.6 59.453 -- 0.0 -- 121943 5975 79.41 -- 0.2059 0.2022 0.245 --
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 3.6 3.6473 -- 67 1047 0.2426 0.2195 -- 14.0
X Ray Diffraction 3.6473 3.7136 -- 101 2230 0.2117 0.1995 -- 30.0
X Ray Diffraction 3.7136 3.785 -- 122 2991 0.2 0.2235 -- 39.0
X Ray Diffraction 3.785 3.8623 -- 195 3591 0.1899 0.228 -- 48.0
X Ray Diffraction 3.8623 3.9462 -- 216 4148 0.1839 0.2276 -- 55.0
X Ray Diffraction 3.9462 4.0379 -- 241 4776 0.1805 0.2126 -- 63.0
X Ray Diffraction 4.0379 4.1388 -- 288 5296 0.1814 0.2309 -- 70.0
X Ray Diffraction 4.1388 4.2507 -- 308 5914 0.1775 0.2208 -- 77.0
X Ray Diffraction 4.2507 4.3756 -- 334 6411 0.1754 0.2175 -- 85.0
X Ray Diffraction 4.3756 4.5168 -- 368 7012 0.163 0.2036 -- 93.0
X Ray Diffraction 4.5168 4.678 -- 381 7236 0.1692 0.2172 -- 95.0
X Ray Diffraction 4.678 4.8651 -- 367 7236 0.1745 0.2357 -- 95.0
X Ray Diffraction 4.8651 5.0863 -- 372 7229 0.18 0.2383 -- 95.0
X Ray Diffraction 5.0863 5.354 -- 386 7175 0.1966 0.2542 -- 95.0
X Ray Diffraction 5.354 5.6889 -- 355 7206 0.2153 0.283 -- 94.0
X Ray Diffraction 5.6889 6.1271 -- 333 7180 0.2254 0.268 -- 94.0
X Ray Diffraction 6.1271 6.7419 -- 373 7276 0.2422 0.3007 -- 95.0
X Ray Diffraction 6.7419 7.7133 -- 363 7268 0.2371 0.2725 -- 95.0
X Ray Diffraction 7.7133 9.7022 -- 402 7236 0.2101 0.2412 -- 93.0
X Ray Diffraction 9.7022 45.2587 -- 403 7436 0.2551 0.2799 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 98.3165
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 5.932
f_bond_d 0.003
f_angle_d 0.634
f_chiral_restr 0.042
f_plane_restr 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 77382
Nucleic Acid Atoms 0
Heterogen Atoms 496
Solvent Atoms 0

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.3.21
PHENIX refinement
PDB_EXTRACT data extraction version: 3.24
PHASER phasing
Coot model building