X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.15
Details 0.1M HEPES pH 7.5, 14% PEG8000, 0.2M Calcium acetate hydrate, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.79 α = 90
b = 39.78 β = 99.75
c = 93.9 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.8726 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
2.2 50 97.4 -- -- -- -- 22844 22248 2.0 2.0 --

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 2.197 46.602 -- 1.99 22844 22245 1117 97.41 -- 0.2141 0.213 0.2338 5% of total reflections, using the Rfree-flag generation in phenix
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 2.197 2.2974 -- 134 2550 0.2603 0.3363 -- 96.0
X Ray Diffraction 2.2974 2.4185 -- 139 2610 0.2538 0.3089 -- 97.0
X Ray Diffraction 2.4185 2.57 -- 136 2618 0.2398 0.2807 -- 98.0
X Ray Diffraction 2.57 2.7684 -- 139 2667 0.2294 0.2775 -- 98.0
X Ray Diffraction 2.7684 3.0469 -- 142 2652 0.2219 0.2371 -- 98.0
X Ray Diffraction 3.0469 3.4877 -- 138 2648 0.2229 0.2493 -- 98.0
X Ray Diffraction 3.4877 4.3936 -- 144 2668 0.1856 0.1897 -- 98.0
X Ray Diffraction 4.3936 46.6121 -- 145 2715 0.192 0.189 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.5957
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.8794
Anisotropic B[2][2] 1.4241
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.0198
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.079
f_dihedral_angle_d 14.148
f_angle_d 1.165
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3089
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 141

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
Xscale Data Reduction (data scaling)
none Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
none model building
DNA data collection