X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 291.0
Details 5% MPD, 20 mM Na Cacodylate, 6 mM Spermine tetra-HCl, 6 mM NaCl, 40 mM KCl , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 25.09 α = 90
b = 41.48 β = 90
c = 65.69 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 300 mm plate -- 2014-04-10
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.000 APS 21-ID-D

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
1.9 50 99.3 0.064 -- -- 10.2 5842 5801 -- -- --
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)
1.9 1.93 100.0 0.738 -- 3.25 6.7 --

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 1.9 35.07 5.0 -- 5842 5362 413 99.35 -- 0.22767 0.22637 0.24529 RANDOM
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 1.897 1.947 380 33 380 0.314 0.337 -- 99.04
RMS Deviations
Key Refinement Restraint Deviation
r_long_range_B_other 7.721
r_chiral_restr 0.08
r_scangle_other 7.896
r_angle_refined_deg 1.333
r_scbond_other 5.991
r_gen_planes_refined 0.026
r_scbond_it 5.987
r_bond_refined_d 0.011
r_bond_other_d 0.002
r_angle_other_deg 1.467
r_gen_planes_other 0.003
r_long_range_B_refined 7.725
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 490
Heterogen Atoms 0
Solvent Atoms 17

Software

Software
Software Name Purpose
MD2 data collection version: diffractometer software from EMBL (with LS-CAT developed extensions)
MOLREP phasing
REFMAC refinement version: 5.8.0069
HKL-2000 data reduction
HKL-2000 data scaling