X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 298.0
Details 100 mM MES, pH 6.0, 36% PEG400, 100 mM BTP , 120 mM sodium chloride

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.07 α = 90
b = 47.44 β = 106.1
c = 53.47 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 -- 2012-10-20
Diffraction Radiation
Monochromator Protocol
cryo-cooled double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.688 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
0.87 28.91 99.8 0.072 -- -- 6.4 -- 159546 -- -- 8.22
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)
0.88 0.89 99.2 2.601 -- 0.4 5.8 --

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 0.92 28.194 -- 1.33 -- 139424 6931 99.66 -- 0.1199 0.1194 0.1295 --
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 0.92 0.9305 -- 221 4392 0.3419 0.3442 -- 99.0
X Ray Diffraction 0.9305 0.9414 -- 193 4398 0.3086 0.3137 -- 100.0
X Ray Diffraction 0.9414 0.9529 -- 263 4398 0.2767 0.2893 -- 100.0
X Ray Diffraction 0.9529 0.9649 -- 227 4372 0.2764 0.2609 -- 100.0
X Ray Diffraction 0.9649 0.9776 -- 226 4443 0.2315 0.2384 -- 100.0
X Ray Diffraction 0.9776 0.991 -- 229 4390 0.2171 0.2218 -- 100.0
X Ray Diffraction 0.991 1.0052 -- 217 4445 0.2027 0.2105 -- 100.0
X Ray Diffraction 1.0052 1.0202 -- 246 4381 0.1804 0.2039 -- 100.0
X Ray Diffraction 1.0202 1.0361 -- 224 4424 0.1652 0.1817 -- 100.0
X Ray Diffraction 1.0361 1.0531 -- 241 4415 0.1533 0.1822 -- 100.0
X Ray Diffraction 1.0531 1.0713 -- 210 4409 0.1395 0.1555 -- 100.0
X Ray Diffraction 1.0713 1.0908 -- 247 4387 0.13 0.1337 -- 100.0
X Ray Diffraction 1.0908 1.1118 -- 212 4336 0.1416 0.1485 -- 98.0
X Ray Diffraction 1.1118 1.1344 -- 214 4451 0.1149 0.1361 -- 100.0
X Ray Diffraction 1.1344 1.1591 -- 235 4328 0.1241 0.1441 -- 99.0
X Ray Diffraction 1.1591 1.1861 -- 211 4463 0.0997 0.1126 -- 100.0
X Ray Diffraction 1.1861 1.2157 -- 242 4412 0.0891 0.1068 -- 100.0
X Ray Diffraction 1.2157 1.2486 -- 200 4455 0.0866 0.1017 -- 100.0
X Ray Diffraction 1.2486 1.2854 -- 249 4372 0.088 0.0979 -- 100.0
X Ray Diffraction 1.2854 1.3268 -- 234 4444 0.0882 0.1096 -- 100.0
X Ray Diffraction 1.3268 1.3743 -- 232 4354 0.0938 0.1197 -- 99.0
X Ray Diffraction 1.3743 1.4293 -- 230 4417 0.0788 0.0909 -- 100.0
X Ray Diffraction 1.4293 1.4943 -- 238 4442 0.0833 0.0925 -- 100.0
X Ray Diffraction 1.4943 1.5731 -- 249 4415 0.0852 0.105 -- 100.0
X Ray Diffraction 1.5731 1.6717 -- 230 4461 0.0839 0.0941 -- 100.0
X Ray Diffraction 1.6717 1.8007 -- 248 4382 0.0883 0.1039 -- 100.0
X Ray Diffraction 1.8007 1.9819 -- 261 4447 0.0917 0.1126 -- 100.0
X Ray Diffraction 1.9819 2.2686 -- 218 4462 0.0999 0.1024 -- 100.0
X Ray Diffraction 2.2686 2.8577 -- 231 4460 0.1126 0.1174 -- 99.0
X Ray Diffraction 2.8577 28.2077 -- 253 4538 0.1375 0.1402 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.067
f_plane_restr 0.008
f_bond_d 0.008
f_chiral_restr 0.092
f_dihedral_angle_d 16.21
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1657
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 306

Software

Software
Software Name Purpose
PHENIX refinement version: (dev_2328: ???)
PDB_EXTRACT data extraction version: 3.15
Coot model building
XDS data scaling
XDS data reduction
Aimless data scaling
PHASER phasing