X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.15
Details 0.79M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 211.99 α = 90
b = 211.99 β = 90
c = 282.77 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) -- PAL/PLS 5C (4A)

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
2.9 20 100.0 -- -- -- -- 162384 n/a -- -- --

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 2.9 19.954 -- 1.34 -- 162245 8134 99.9 -- 0.1996 0.1975 0.2383 --
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 2.896 2.9288 -- 275 4986 0.3283 0.3943 -- 99.0
X Ray Diffraction 2.9288 2.9632 -- 254 5148 0.3154 0.3822 -- 100.0
X Ray Diffraction 2.9632 2.9992 -- 287 5077 0.3057 0.3755 -- 100.0
X Ray Diffraction 2.9992 3.037 -- 252 5098 0.2989 0.3657 -- 100.0
X Ray Diffraction 3.037 3.0769 -- 274 5100 0.276 0.3561 -- 100.0
X Ray Diffraction 3.0769 3.1189 -- 266 5097 0.2729 0.3036 -- 100.0
X Ray Diffraction 3.1189 3.1632 -- 281 5092 0.2763 0.3313 -- 100.0
X Ray Diffraction 3.1632 3.2103 -- 265 5129 0.2716 0.314 -- 100.0
X Ray Diffraction 3.2103 3.2602 -- 257 5085 0.2456 0.2948 -- 100.0
X Ray Diffraction 3.2602 3.3134 -- 287 5116 0.2272 0.2616 -- 100.0
X Ray Diffraction 3.3134 3.3703 -- 256 5120 0.2334 0.3006 -- 100.0
X Ray Diffraction 3.3703 3.4313 -- 257 5133 0.2181 0.2632 -- 100.0
X Ray Diffraction 3.4313 3.497 -- 291 5060 0.219 0.264 -- 100.0
X Ray Diffraction 3.497 3.5679 -- 252 5140 0.2298 0.3024 -- 100.0
X Ray Diffraction 3.5679 3.6451 -- 282 5125 0.2292 0.2696 -- 100.0
X Ray Diffraction 3.6451 3.7293 -- 255 5110 0.2094 0.2723 -- 100.0
X Ray Diffraction 3.7293 3.822 -- 268 5129 0.2048 0.256 -- 100.0
X Ray Diffraction 3.822 3.9245 -- 266 5155 0.1933 0.2472 -- 100.0
X Ray Diffraction 3.9245 4.0391 -- 252 5096 0.1823 0.2261 -- 100.0
X Ray Diffraction 4.0391 4.1683 -- 276 5153 0.1691 0.2098 -- 100.0
X Ray Diffraction 4.1683 4.3159 -- 273 5129 0.1546 0.2017 -- 100.0
X Ray Diffraction 4.3159 4.4868 -- 255 5147 0.1556 0.2035 -- 100.0
X Ray Diffraction 4.4868 4.6885 -- 275 5174 0.1568 0.1979 -- 100.0
X Ray Diffraction 4.6885 4.9321 -- 281 5142 0.1523 0.1847 -- 100.0
X Ray Diffraction 4.9321 5.2359 -- 242 5198 0.1542 0.187 -- 100.0
X Ray Diffraction 5.2359 5.6317 -- 276 5170 0.161 0.2028 -- 100.0
X Ray Diffraction 5.6317 6.1831 -- 285 5196 0.1843 0.2125 -- 100.0
X Ray Diffraction 6.1831 7.0432 -- 273 5235 0.1988 0.2478 -- 100.0
X Ray Diffraction 7.0432 8.7474 -- 302 5245 0.165 0.1755 -- 100.0
X Ray Diffraction 8.7474 19.9543 -- 319 5326 0.1657 0.1745 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.009
f_chiral_restr 0.094
f_dihedral_angle_d 20.309
f_angle_d 1.913
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 23648
Nucleic Acid Atoms 4064
Heterogen Atoms 0
Solvent Atoms 209

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1168) refinement
PHENIX model building
HKL-2000 data collection