X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.1
Temperature 291.0
Details 0.1 M imidazole/MES, pH 6.1, 20% glycerol, 10% PEG4000, 126 mM halogens (sodium iodide, sodium bromide, sodium fluoride), 10 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.02 α = 90
b = 77.09 β = 90.71
c = 81.83 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
CCD ADSC QUANTUM 315r -- 2012-06-04
Diffraction Radiation
Monochromator Protocol
channel cut Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9394 ESRF ID14-4

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
1.94 45.34 99.5 0.093 -- -- 5.0 49786 49569 2.0 2.0 --
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)
1.94 -- 99.2 0.086 -- 2.28 5.0 --

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 1.94 45.337 -- 2.0 49786 49569 2001 99.54 -- 0.181 0.1792 0.2257 --
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 1.94 1.9884 -- 134 3359 0.2175 0.272 -- 99.0
X Ray Diffraction 1.9884 2.0422 -- 142 3396 0.2079 0.2323 -- 99.0
X Ray Diffraction 2.0422 2.1023 -- 148 3348 0.1985 0.2799 -- 99.0
X Ray Diffraction 2.1023 2.1701 -- 147 3359 0.1963 0.2709 -- 100.0
X Ray Diffraction 2.1701 2.2477 -- 133 3422 0.1972 0.2723 -- 99.0
X Ray Diffraction 2.2477 2.3377 -- 150 3392 0.1881 0.2605 -- 100.0
X Ray Diffraction 2.3377 2.4441 -- 148 3371 0.1854 0.2603 -- 100.0
X Ray Diffraction 2.4441 2.5729 -- 131 3424 0.1847 0.2512 -- 100.0
X Ray Diffraction 2.5729 2.7341 -- 146 3376 0.1947 0.2747 -- 100.0
X Ray Diffraction 2.7341 2.9452 -- 156 3395 0.1899 0.229 -- 100.0
X Ray Diffraction 2.9452 3.2415 -- 141 3418 0.1839 0.2227 -- 100.0
X Ray Diffraction 3.2415 3.7103 -- 145 3414 0.1619 0.204 -- 100.0
X Ray Diffraction 3.7103 4.6739 -- 140 3439 0.1494 0.1689 -- 100.0
X Ray Diffraction 4.6739 45.3497 -- 140 3455 0.1816 0.2185 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.078
f_dihedral_angle_d 15.364
f_angle_d 1.077
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5111
Nucleic Acid Atoms 78
Heterogen Atoms 6
Solvent Atoms 356

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XDS package Data Reduction (intensity integration)
XDS package Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1168) refinement
PHASER model building
ADSC version: Quantum data collection