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_dihedral_angle_d 19.003
f_angle_d 1.07
f_chiral_restr 0.065
f_bond_d 0.007
f_plane_restr 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

Software
Software Name Purpose
SAINT data scaling
PHENIX refinement
PDB_EXTRACT data extraction version: 3.11
APEX data collection
SAINT data reduction
XPREP data reduction
PHASER phasing