X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 304.0
Details 50 mM sodium cacodylate, 5-6% isopropanol, optimised mixture of salts, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 304K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 158.55 α = 90
b = 158.55 β = 90
c = 210.33 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
CCD ADSC QUANTUM 315 -- 2010-08-05
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 0.9762 DIAMOND I04

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
2.71 114.98 99.9 0.239 0.239 -- 6.0 83475 83426 0.0 0.0 66.392
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)
2.71 2.78 100.0 1.936 -- 0.4 6.1 6122

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 3.24 114.977 -- 1.44 49022 49022 1505 99.77 0.1681 0.1681 0.1668 0.2064 RANDOM
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 3.2401 3.3447 -- 131 4252 0.2137 0.2527 -- 100.0
X Ray Diffraction 3.3447 3.4643 -- 140 4281 0.1891 0.2611 -- 100.0
X Ray Diffraction 3.4643 3.603 -- 133 4293 0.1782 0.236 -- 100.0
X Ray Diffraction 3.603 3.767 -- 136 4281 0.1625 0.1859 -- 100.0
X Ray Diffraction 3.767 3.9656 -- 136 4281 0.15 0.221 -- 100.0
X Ray Diffraction 3.9656 4.2141 -- 134 4279 0.1419 0.1837 -- 100.0
X Ray Diffraction 4.2141 4.5394 -- 139 4336 0.136 0.1626 -- 100.0
X Ray Diffraction 4.5394 4.9963 -- 138 4319 0.1386 0.1762 -- 100.0
X Ray Diffraction 4.9963 5.7192 -- 138 4353 0.1562 0.2262 -- 100.0
X Ray Diffraction 5.7192 7.2055 -- 142 4360 0.1816 0.1973 -- 100.0
X Ray Diffraction 7.2055 115.049 -- 138 4482 0.1788 0.1941 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.1955
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.1955
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -18.9756
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.075
f_dihedral_angle_d 18.003
f_angle_d 1.283
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10403
Nucleic Acid Atoms 730
Heterogen Atoms 56
Solvent Atoms 40

Software

Computing
Computing Package Purpose
GDE Data Collection
XIA2 (mosflm) Data Reduction (intensity integration)
XIA2 (scala) Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.6.1_357) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.1_357) refinement
Phaser model building
GDE data collection