X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5
Temperature 298.0
Details 0.1 M sodium cacodylate, 0.1 M calcium acetate, 10% PEG 8,000, pH 5.0, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 223.87 α = 90
b = 223.87 β = 90
c = 290.65 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2014-01-20
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen-cooled double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 1.2131 SSRL BL12-2

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
3.03 39.47 99.8 -- -- -- -- 16404 163355 0.0 -3.7 --
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)
3.03 3.05 96.4 -- -- -- -- --

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
SAD 3.0303 39.473 -- 1.33 -- 156727 7915 96.2 -- 0.2257 0.2235 0.2672 --
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 3.0303 3.0647 -- 260 4580 0.322 0.3618 -- 90.0
X Ray Diffraction 3.0647 3.1008 -- 284 5005 0.3098 0.3483 -- 99.0
X Ray Diffraction 3.1008 3.1386 -- 254 5085 0.2962 0.3589 -- 99.0
X Ray Diffraction 3.1386 3.1783 -- 275 5059 0.2872 0.3313 -- 99.0
X Ray Diffraction 3.1783 3.2201 -- 252 5094 0.3045 0.3532 -- 99.0
X Ray Diffraction 3.2201 3.2642 -- 271 5090 0.3245 0.3878 -- 99.0
X Ray Diffraction 3.2642 3.3108 -- 262 5092 0.3119 0.3642 -- 99.0
X Ray Diffraction 3.3108 3.3602 -- 266 5114 0.3038 0.365 -- 100.0
X Ray Diffraction 3.3602 3.4127 -- 250 4415 0.4267 0.5165 -- 87.0
X Ray Diffraction 3.4127 3.4686 -- 220 4027 0.4857 0.562 -- 78.0
X Ray Diffraction 3.4686 3.5283 -- 286 5061 0.2923 0.3402 -- 99.0
X Ray Diffraction 3.5283 3.5925 -- 285 5074 0.2441 0.2841 -- 99.0
X Ray Diffraction 3.5925 3.6615 -- 225 4153 0.4183 0.4992 -- 81.0
X Ray Diffraction 3.6615 3.7362 -- 230 4330 0.4096 0.4766 -- 84.0
X Ray Diffraction 3.7362 3.8174 -- 252 5109 0.2592 0.299 -- 100.0
X Ray Diffraction 3.8174 3.9061 -- 235 4441 0.4475 0.5621 -- 86.0
X Ray Diffraction 3.9061 4.0037 -- 243 4599 0.2545 0.3164 -- 90.0
X Ray Diffraction 4.0037 4.1118 -- 265 5103 0.1787 0.2201 -- 99.0
X Ray Diffraction 4.1118 4.2327 -- 283 5110 0.1684 0.2171 -- 99.0
X Ray Diffraction 4.2327 4.3691 -- 284 5132 0.1554 0.1932 -- 100.0
X Ray Diffraction 4.3691 4.5251 -- 250 5136 0.1505 0.1861 -- 99.0
X Ray Diffraction 4.5251 4.706 -- 252 5145 0.1392 0.1694 -- 100.0
X Ray Diffraction 4.706 4.9198 -- 312 5115 0.1376 0.1674 -- 100.0
X Ray Diffraction 4.9198 5.1786 -- 261 5190 0.1504 0.1872 -- 100.0
X Ray Diffraction 5.1786 5.5023 -- 288 5170 0.1628 0.2128 -- 100.0
X Ray Diffraction 5.5023 5.9258 -- 278 5207 0.173 0.2327 -- 100.0
X Ray Diffraction 5.9258 6.5198 -- 233 5229 0.1751 0.2122 -- 100.0
X Ray Diffraction 6.5198 7.4577 -- 273 5274 0.175 0.2167 -- 100.0
X Ray Diffraction 7.4577 9.3751 -- 293 5250 0.152 0.1756 -- 100.0
X Ray Diffraction 9.3751 39.4766 -- 293 5423 0.1959 0.2051 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.061
f_bond_d 0.012
f_dihedral_angle_d 20.092
f_angle_d 1.524
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 24694
Nucleic Acid Atoms 1848
Heterogen Atoms 1
Solvent Atoms 0

Software

Software
Software Name Purpose
Blu-Ice data collection
SOLVE phasing
PHENIX refinement version: (phenix.refine: 1.9_1692)
XDS data reduction
Aimless data scaling