X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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_bond_d 0.014
f_chiral_restr 0.082
f_angle_d 1.849
f_plane_restr 0.015
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

Software
Software Name Purpose
BSS data collection
AMoRE phasing
PHENIX refinement version: (phenix.refine: 1.6.4_486)
MOSFLM data reduction
SCALA data scaling