X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.4
Temperature 293.0
Details 2.0 M ammonium sulfate, 0.1 M sodium acetate, 7.5 % glycerol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.91 α = 90
b = 110.91 β = 90
c = 43.14 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 70
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PILATUS 6M-F -- 2012-09-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.97 ESRF ID23-1

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
1.8 32.55 96.4 0.074 -- -- 4.6 -- 12161 -- 2.0 27.1
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)
1.8 1.9 96.0 0.679 -- 2.2 4.7 --

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 1.8 28.072 -- 1.35 -- 12155 1216 94.99 -- 0.1841 0.1809 0.2116 lattice symmetry 10%
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 1.8 1.8721 -- 131 1188 0.2328 0.2574 -- 95.0
X Ray Diffraction 1.8721 1.9573 -- 133 1188 0.2237 0.251 -- 95.0
X Ray Diffraction 1.9573 2.0604 -- 131 1178 0.2019 0.2436 -- 95.0
X Ray Diffraction 2.0604 2.1895 -- 135 1213 0.1877 0.23 -- 96.0
X Ray Diffraction 2.1895 2.3584 -- 135 1211 0.1793 0.2112 -- 96.0
X Ray Diffraction 2.3584 2.5956 -- 136 1231 0.1893 0.2229 -- 97.0
X Ray Diffraction 2.5956 2.9709 -- 138 1241 0.1948 0.2175 -- 97.0
X Ray Diffraction 2.9709 3.7416 -- 139 1244 0.1662 0.2 -- 96.0
X Ray Diffraction 3.7416 28.0754 -- 138 1245 0.1667 0.1939 -- 90.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.009
f_chiral_restr 0.138
f_dihedral_angle_d 19.133
f_angle_d 2.062
f_bond_d 0.019
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 535
Nucleic Acid Atoms 123
Heterogen Atoms 0
Solvent Atoms 73

Software

Computing
Computing Package Purpose
DNA Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.2_1309) refinement
PHASER model building
DNA data collection