X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Temperature Control
pH 7
Temperature 293.0
Details 2.0mM DNA, 20mM Na cacodylate, 30% 2-methyl-2,4-pentainediol, 500mM MgCl2, pH 7.0, TEMPERATURE CONTROL, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 18.59 α = 90
b = 18.59 β = 90
c = 72.7 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2008-02-13
Diffraction Radiation
Monochromator Protocol
Fixed exit Si (111) double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1 SPRING-8 BL38B1

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 24.2 99.2 0.054 -- -- 6.6 6915 6868 0.0 0.0 12.3
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 99.0 0.12 -- -- 6.6 1006

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 1.3 9.682 -- 0.16 -- 6815 322 98.6 -- 0.2133 0.2109 0.2635 RABDOM
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 1.3001 1.6366 -- 162 3235 0.2038 0.2744 -- 98.0
X Ray Diffraction 1.6366 9.682 -- 160 3258 0.2129 0.2601 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.8432
Anisotropic B[1][1] -0.5405
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.5405
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.0809
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 29.583
f_plane_restr 0.015
f_chiral_restr 0.082
f_angle_d 1.849
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 240
Heterogen Atoms 14
Solvent Atoms 73

Software

Computing
Computing Package Purpose
BSS Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
AMoRE Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
AMoRE model building
BSS data collection