X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Temperature 293.0
Details The complex crystallized spontaneously at a concentration of 0.5 mM in the NMR buffer (10 mM Na-Phosphate buffer pH 6.5, 50 mM NaCl), BATCH, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.05 α = 90
b = 36.48 β = 92.48
c = 73.37 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 2M-F -- 2013-04-30
Diffraction Radiation
Monochromator Protocol
FIXED EXIT DOUBLE, CHANNEL DCM MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 0.80000 SLS X06DA

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
1.2 35.08 100.0 0.043 -- -- 13.3 -- 64851 -- -3.0 12.5
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)
1.2 1.3 100.0 0.657 -- 4.38 -- --

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 1.2 35.075 -- 1.36 -- 64837 972 99.96 -- 0.1474 0.1471 0.1648 --
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 1.2 1.2633 -- 138 9087 0.1539 0.1913 -- 100.0
X Ray Diffraction 1.2633 1.3424 -- 138 9044 0.1306 0.1742 -- 100.0
X Ray Diffraction 1.3424 1.4461 -- 138 9082 0.1196 0.1736 -- 100.0
X Ray Diffraction 1.4461 1.5916 -- 138 9082 0.1044 0.1288 -- 100.0
X Ray Diffraction 1.5916 1.8219 -- 138 9113 0.1151 0.1404 -- 100.0
X Ray Diffraction 1.8219 2.2954 -- 140 9153 0.1459 0.1402 -- 100.0
X Ray Diffraction 2.2954 35.0905 -- 142 9304 0.1682 0.1843 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.3977
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.066
f_dihedral_angle_d 16.387
f_angle_d 0.994
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1503
Nucleic Acid Atoms 268
Heterogen Atoms 4
Solvent Atoms 207

Software

Computing
Computing Package Purpose
DA+ Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.4_1496) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction