X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 291.0
Details 0.1 M Bicine, 12% PEG3350, 10 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.14 α = 82.26
b = 74.77 β = 72.57
c = 116.99 γ = 82.4
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2009-12-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.93340 ESRF ID14-1

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 58.77 97.8 0.073 0.073 -- 3.9 45027 45027 0.0 0.0 91.64
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)
3.0 3.16 97.5 0.921 0.921 1.5 3.9 6546

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 3.0 55.526 -- 0.0 45009 45009 2264 97.79 -- 0.2555 0.2539 0.2848 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 3.0 3.0652 -- 124 2660 0.3691 0.4168 -- 98.0
X Ray Diffraction 3.0652 3.1365 -- 127 2694 0.3456 0.3415 -- 97.0
X Ray Diffraction 3.1365 3.215 -- 149 2641 0.3264 0.3823 -- 98.0
X Ray Diffraction 3.215 3.3019 -- 141 2633 0.322 0.377 -- 97.0
X Ray Diffraction 3.3019 3.399 -- 149 2695 0.3066 0.3249 -- 98.0
X Ray Diffraction 3.399 3.5087 -- 151 2642 0.3036 0.3577 -- 98.0
X Ray Diffraction 3.5087 3.6341 -- 126 2694 0.3013 0.3628 -- 98.0
X Ray Diffraction 3.6341 3.7796 -- 144 2685 0.3004 0.3258 -- 98.0
X Ray Diffraction 3.7796 3.9515 -- 148 2661 0.2824 0.3522 -- 98.0
X Ray Diffraction 3.9515 4.1598 -- 129 2693 0.275 0.3064 -- 98.0
X Ray Diffraction 4.1598 4.4203 -- 160 2670 0.249 0.3041 -- 98.0
X Ray Diffraction 4.4203 4.7615 -- 157 2653 0.2301 0.2591 -- 98.0
X Ray Diffraction 4.7615 5.2403 -- 145 2676 0.2298 0.2289 -- 98.0
X Ray Diffraction 5.2403 5.9978 -- 138 2681 0.24 0.3015 -- 98.0
X Ray Diffraction 5.9978 7.5536 -- 137 2702 0.2345 0.2451 -- 98.0
X Ray Diffraction 7.5536 55.5359 -- 139 2665 0.1988 0.2163 -- 97.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.047
f_dihedral_angle_d 13.545
f_angle_d 0.766
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13238
Nucleic Acid Atoms 672
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_1078) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: dev_1078) refinement
PHASER model building
ADSC version: Quantum data collection