X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 0.1 M imidazole, 9% (w/v) PEG 8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.94 α = 90
b = 43.94 β = 90
c = 120.07 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Toroidal mirror 2009-07-27
Diffraction Radiation
Monochromator Protocol
Diamond (111) and Ge (220) crystals SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2

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
2.2 43.94 99.7 0.042 -- -- 7.7 -- 6500 -- -- --
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)
2.2 2.32 98.1 0.511 -- 3.3 7.1 884

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 2.2 41.268 -- 1.38 -- 6431 631 99.23 -- 0.2233 0.2176 0.277 --
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 2.2 2.3703 -- 117 1093 0.2531 0.3929 -- 98.0
X Ray Diffraction 2.3703 2.6088 -- 130 1129 0.2404 0.3418 -- 99.0
X Ray Diffraction 2.6088 2.9862 -- 127 1141 0.237 0.3065 -- 100.0
X Ray Diffraction 2.9862 3.7619 -- 134 1163 0.2096 0.2762 -- 100.0
X Ray Diffraction 3.7619 41.2753 -- 123 1274 0.2095 0.2452 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 7.7843
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 7.7843
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -15.5686
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.057
f_dihedral_angle_d 15.088
f_angle_d 1.01
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 825
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 10

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
BALBES Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
BALBES model building
DNA data collection