X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.2
Temperature 293.0
Details 1.7 M ammonium sulfate, 0.1 M sodium acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.86 α = 90
b = 56.86 β = 90
c = 218.77 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 70
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PILATUS 6M-F -- 2012-09-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.97 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 29.3 -- 0.088 -- -- 7.3 -- 15007 -- 2.0 34.88
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)
2.0 2.11 100.0 0.53 -- 3.7 7.2 --

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
PDB ENTRY 1QBJ 2.0 29.3 -- 1.34 -- 15006 1501 99.46 -- 0.1915 0.1879 0.2243 lattice symmetry 10%
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 2.0 2.0646 -- 133 1197 0.2308 0.2681 -- 100.0
X Ray Diffraction 2.0646 2.1383 -- 132 1188 0.2126 0.2806 -- 100.0
X Ray Diffraction 2.1383 2.2239 -- 132 1192 0.1925 0.2469 -- 100.0
X Ray Diffraction 2.2239 2.3251 -- 134 1205 0.1993 0.2404 -- 100.0
X Ray Diffraction 2.3251 2.4476 -- 135 1209 0.1872 0.2571 -- 100.0
X Ray Diffraction 2.4476 2.6009 -- 135 1224 0.2059 0.2253 -- 100.0
X Ray Diffraction 2.6009 2.8016 -- 136 1212 0.2186 0.2443 -- 100.0
X Ray Diffraction 2.8016 3.0832 -- 136 1229 0.1989 0.2554 -- 100.0
X Ray Diffraction 3.0832 3.5287 -- 139 1251 0.1783 0.2082 -- 100.0
X Ray Diffraction 3.5287 4.4433 -- 141 1265 0.1561 0.1903 -- 100.0
X Ray Diffraction 4.4433 29.3061 -- 148 1333 0.1953 0.2194 -- 95.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.074
f_dihedral_angle_d 18.351
f_chiral_restr 0.067
f_plane_restr 0.004
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 999
Nucleic Acid Atoms 247
Heterogen Atoms 12
Solvent Atoms 110

Software

Software
Software Name Purpose
DNA data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.8.1_1168)
MOSFLM data reduction
SCALA data scaling