X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.15
Details 7% PEG 4000, 5mM Magnesium acetate, 50mM N-(2-acetamido)iminodiacetic acid, pH 6.5, vapor diffusion, hanging drop, temperature 293.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.96 α = 90
b = 145.72 β = 90
c = 46.88 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD APEX II CCD -- 2012-07-27
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SEALED TUBE OTHER 1.5418 -- --

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
2.14 33.73 93.7 0.047 -- -- 3.75 21193 19858 0.0 0.0 19.05

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 2.14 33.73 -- 0.0 21193 19139 398 90.6 -- 0.202 0.201 0.239 --
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 2.14 2.4496 -- 103 5189 0.1973 0.2397 -- 77.0
X Ray Diffraction 2.4496 3.0859 -- 152 6521 0.1981 0.2403 -- 96.0
X Ray Diffraction 3.0859 33.7348 -- 143 7031 0.2017 0.2367 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.54
Anisotropic B[1][1] -1.5493
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.3218
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.8957
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.065
f_dihedral_angle_d 19.003
f_angle_d 1.07
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2019
Nucleic Acid Atoms 325
Heterogen Atoms 16
Solvent Atoms 148

Software

Computing
Computing Package Purpose
APEX Data Collection
SAINT Data Reduction (intensity integration)
XPREP Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SAINT data collection