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 DECTRIS PILATUS 2M 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_dihedral_angle_d 30.264
f_angle_d 2.087
f_bond_d 0.017
f_chiral_restr 0.099
f_plane_restr 0.035
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

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE)
XDS data reduction
SCALA data scaling
PHASER phasing