X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 295.0
Details 100 mM Bis-Tris pH 6.0, 26% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 0.6% DDM, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 295.0
Details 100 mM Bis-Tris pH 6.0, 24% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 50 mM NDSB-201, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 295.0
Details 100 mM Bis-Tris pH 6.0, 19% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 2.2 mM FOS-CHOLINE-8 fluorinated , VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.28 α = 90
b = 340.89 β = 100.57
c = 263.3 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
3 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M mirrors 2011-02-16
PIXEL PSI PILATUS 6M mirrors 2011-12-03
PIXEL PSI PILATUS 6M mirrors 2011-09-23
Diffraction Radiation
Monochromator Protocol
Si(311) SINGLE WAVELENGTH
Si(311) SINGLE WAVELENGTH
Si(311) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.9 ESRF ID29
SYNCHROTRON ESRF BEAMLINE ID29 0.9 ESRF ID29
SYNCHROTRON ESRF BEAMLINE ID29 0.9 ESRF ID29

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
3.3 40 99.5 0.251 0.251 -- 6.1 247920 247920 0.0 0.0 99.0
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)
3.3 3.48 99.0 1.869 1.869 1.0 5.6 --

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 3.3027 39.998 -- 0.0 233383 233383 2427 93.66 -- 0.2034 0.2024 0.2393 Random, using lattice symmetry information (PHENIX).
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 3.3027 3.37 -- 67 5388 0.2842 0.3081 -- 37.0
X Ray Diffraction 3.37 3.4432 -- 97 10229 0.2653 0.3046 -- 70.0
X Ray Diffraction 3.4432 3.5232 -- 139 13541 0.2485 0.3042 -- 94.0
X Ray Diffraction 3.5232 3.6112 -- 157 14324 0.2402 0.2692 -- 98.0
X Ray Diffraction 3.6112 3.7088 -- 143 14430 0.2338 0.3029 -- 98.0
X Ray Diffraction 3.7088 3.8178 -- 158 14297 0.223 0.2564 -- 99.0
X Ray Diffraction 3.8178 3.9408 -- 143 14299 0.2221 0.257 -- 98.0
X Ray Diffraction 3.9408 4.0814 -- 148 14375 0.2096 0.2649 -- 98.0
X Ray Diffraction 4.0814 4.2446 -- 144 14397 0.2056 0.2223 -- 98.0
X Ray Diffraction 4.2446 4.4373 -- 157 14365 0.1929 0.222 -- 98.0
X Ray Diffraction 4.4373 4.6707 -- 153 14381 0.188 0.2461 -- 98.0
X Ray Diffraction 4.6707 4.9625 -- 161 14426 0.1844 0.2297 -- 99.0
X Ray Diffraction 4.9625 5.3443 -- 163 14429 0.1898 0.2227 -- 99.0
X Ray Diffraction 5.3443 5.8796 -- 151 14372 0.1966 0.2355 -- 99.0
X Ray Diffraction 5.8796 6.7247 -- 152 14496 0.1941 0.199 -- 99.0
X Ray Diffraction 6.7247 8.4507 -- 120 14515 0.1689 0.2179 -- 99.0
X Ray Diffraction 8.4507 33.9226 -- 164 14580 0.1915 0.2142 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS and isotropic
Mean Isotropic B 74.4
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.111
f_dihedral_angle_d 18.03
f_angle_d 1.467
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 73808
Nucleic Acid Atoms 0
Heterogen Atoms 190
Solvent Atoms 0

Software

Computing
Computing Package Purpose
MOSFLM Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_1041) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: dev_1041) refinement
PHASER model building
MOSFLM data collection