X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details 40% MPD, SPERMINE, MAGNESIUM CHLORIDE, SODIUM CACODYLATE PH 7.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 25.15 α = 90
b = 39.84 β = 90
c = 65.6 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL (PILATUS 2M) DECTRIS MIRRORS 2011-08-05
Diffraction Radiation
Monochromator Protocol
SI (111) DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 -- DIAMOND I04-1

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
1.3 25.32 98.0 0.03 -- -- 6.3 -- 16471 -- 0.0 16.78
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)
1.3 1.37 95.9 0.22 -- 6.1 5.1 --

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 1.32 25.322 -- 0.0 -- 15416 1516 95.62 -- 0.1426 0.1385 0.1823 --
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 1.3201 1.3627 -- 126 1127 0.1777 0.2526 -- 88.0
X Ray Diffraction 1.3627 1.4114 -- 132 1185 0.1614 0.2391 -- 91.0
X Ray Diffraction 1.4114 1.4679 -- 128 1225 0.1382 0.2079 -- 93.0
X Ray Diffraction 1.4679 1.5347 -- 129 1171 0.1344 0.1797 -- 91.0
X Ray Diffraction 1.5347 1.6156 -- 136 1258 0.1204 0.1832 -- 97.0
X Ray Diffraction 1.6156 1.7168 -- 137 1266 0.107 0.1799 -- 97.0
X Ray Diffraction 1.7168 1.8493 -- 141 1293 0.1083 0.1608 -- 98.0
X Ray Diffraction 1.8493 2.0353 -- 142 1299 0.1292 0.1787 -- 98.0
X Ray Diffraction 2.0353 2.3296 -- 143 1314 0.1415 0.2268 -- 99.0
X Ray Diffraction 2.3296 2.9344 -- 147 1343 0.1571 0.1948 -- 99.0
X Ray Diffraction 2.9344 25.3264 -- 155 1419 0.1406 0.1607 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.78
Anisotropic B[1][1] -1.0359
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.5813
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.4545
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.035
f_chiral_restr 0.099
f_dihedral_angle_d 30.264
f_angle_d 2.087
f_bond_d 0.017
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 486
Heterogen Atoms 1
Solvent Atoms 131

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
PHASER model building