X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.5
Temperature 296.0
Details MPD, MgCl2, NaCl, KCL, spermine, pH 6.5, VAPOR DIFFUSION, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 30.23 α = 90
b = 30.23 β = 90
c = 119.25 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD PILATUS 2M -- 2011-03-13
Diffraction Radiation
Monochromator Protocol
double-crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.000 ELETTRA 5.2R

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
2.1 30 99.0 0.089 -- -- -- -- 4087 -- -3.0 46.83
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)
2.1 2.23 97.8 0.226 -- 5.34 -- --

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 2.1 20.0 -- 0.0 -- 4087 209 93.9 -- -- 0.2196 0.314 Reflections were chosen in thin resolution shells
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 2.1 2.19 -- -- -- 0.373 -- -- 85.29
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 54.1262
RMS Deviations
Key Refinement Restraint Deviation
s_non_zero_chiral_vol 0.005
s_angle_d 0.026
s_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 450
Heterogen Atoms 27
Solvent Atoms 11

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
MOLREP Structure Solution
SHELXH Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
SHELX refinement
MOLREP molecular replacement
Xscale data reduction