X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 290.0
Details 0.1M BIS-TRIS PROPANE pH 6.5, 0.2 M SODIUM FLUORIDE, 20% (w/v) PEG 3350, vapor diffusion, hanging drop, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.37 α = 90
b = 62.37 β = 90
c = 11.73 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2010-12-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97911 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
0.97 14.98 99.3 0.069 -- -- -- -- n/a -- -3.0 9.162
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)
0.97 1.0 97.4 0.448 -- 2.42 -- --

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
SIRAS 0.97 14.981 -- 2.01 -- 15997 1601 99.84 -- 0.1138 0.1119 0.1311 --
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 0.9703 1.0016 -- 140 1251 0.1495 0.1713 -- 99.0
X Ray Diffraction 1.0016 1.0374 -- 144 1303 0.1342 0.1571 -- 100.0
X Ray Diffraction 1.0374 1.0789 -- 145 1301 0.1072 0.1138 -- 100.0
X Ray Diffraction 1.0789 1.128 -- 142 1278 0.0908 0.1088 -- 100.0
X Ray Diffraction 1.128 1.1874 -- 144 1299 0.0891 0.1048 -- 100.0
X Ray Diffraction 1.1874 1.2618 -- 144 1291 0.0941 0.1198 -- 100.0
X Ray Diffraction 1.2618 1.3592 -- 146 1316 0.0961 0.1238 -- 100.0
X Ray Diffraction 1.3592 1.4958 -- 146 1314 0.0982 0.1029 -- 100.0
X Ray Diffraction 1.4958 1.712 -- 147 1320 0.1003 0.1325 -- 100.0
X Ray Diffraction 1.712 2.1559 -- 147 1330 0.1075 0.1349 -- 100.0
X Ray Diffraction 2.1559 14.9826 -- 156 1393 0.1304 0.1445 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.9748
Anisotropic B[1][1] 0.2207
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.2207
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.4415
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.613
f_plane_restr 0.009
f_chiral_restr 0.095
f_angle_d 1.417
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 244
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 49

Software

Computing
Computing Package Purpose
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Xscale data reduction