X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 290.0
Details PEG 4000, sodium cacodylate, zinc chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 127.52 α = 90
b = 127.52 β = 90
c = 89.73 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.934 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
2.7 36.81 -- -- -- -- -- -- 21591 -- -- --

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 2.7 36.8 -- 1.34 -- 21591 1089 91.99 -- 0.2333 0.2307 0.2845 --
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 2.7 2.8229 -- 76 1569 0.354 0.3533 -- 57.0
X Ray Diffraction 2.8229 2.9717 -- 127 2251 0.3577 0.3617 -- 82.0
X Ray Diffraction 2.9717 3.1578 -- 141 2736 0.3296 0.3868 -- 100.0
X Ray Diffraction 3.1578 3.4014 -- 164 2751 0.2945 0.3563 -- 100.0
X Ray Diffraction 3.4014 3.7434 -- 149 2770 0.2475 0.3287 -- 100.0
X Ray Diffraction 3.7434 4.2844 -- 147 2757 0.2217 0.2652 -- 99.0
X Ray Diffraction 4.2844 5.3951 -- 134 2811 0.1867 0.2415 -- 100.0
X Ray Diffraction 5.3951 36.8153 -- 151 2857 0.2017 0.2419 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.2829
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.2829
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.5657
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_chiral_restr 0.095
f_dihedral_angle_d 19.287
f_angle_d 1.733
f_bond_d 0.026
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6383
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 12

Software

Computing
Computing Package Purpose
DNA Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.6.1_357) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.1_357) refinement
PHASER model building
DNA data collection