X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 283.0
Details 95 mM trisodium citrate, pH 5.6-5.9, 6.5-7.0% (v/v) isopropanol, 16.5-18.0% (w/v) PEG4000, 5% (v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 283K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.4 α = 83.72
b = 60.41 β = 83.69
c = 191.43 γ = 77.85
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NOIR-1 -- 2009-05-24
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock Si(111) sagitally focused monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.00 ALS 4.2.2

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
2.3 40.27 97.1 0.073 -- -- 2.09 -- 112942 -- -- --
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)
2.3 2.38 96.4 0.495 -- 1.4 1.91 --

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 2.5 38.622 -- 0.01 -- 85118 4278 93.94 -- 0.2146 0.2116 0.2688 5% 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 2.5 2.5284 -- 141 2634 0.429 0.4681 -- 90.0
X Ray Diffraction 2.5284 2.5581 -- 135 2521 0.4289 0.4733 -- 90.0
X Ray Diffraction 2.5581 2.5893 -- 140 2564 0.3787 0.482 -- 90.0
X Ray Diffraction 2.5893 2.6221 -- 123 2699 0.3795 0.4562 -- 90.0
X Ray Diffraction 2.6221 2.6566 -- 134 2469 0.3951 0.473 -- 90.0
X Ray Diffraction 2.6566 2.693 -- 131 2557 0.3653 0.4887 -- 90.0
X Ray Diffraction 2.693 2.7314 -- 112 2685 0.346 0.4625 -- 91.0
X Ray Diffraction 2.7314 2.7722 -- 129 2589 0.3274 0.3591 -- 91.0
X Ray Diffraction 2.7722 2.8155 -- 140 2653 0.3285 0.4054 -- 92.0
X Ray Diffraction 2.8155 2.8617 -- 119 2761 0.3064 0.3996 -- 93.0
X Ray Diffraction 2.8617 2.911 -- 130 2624 0.2823 0.3776 -- 93.0
X Ray Diffraction 2.911 2.9639 -- 136 2659 0.2749 0.3836 -- 94.0
X Ray Diffraction 2.9639 3.0209 -- 147 2807 0.2589 0.3682 -- 94.0
X Ray Diffraction 3.0209 3.0825 -- 149 2643 0.2408 0.3017 -- 95.0
X Ray Diffraction 3.0825 3.1495 -- 169 2728 0.2366 0.2918 -- 95.0
X Ray Diffraction 3.1495 3.2227 -- 138 2713 0.2433 0.2975 -- 96.0
X Ray Diffraction 3.2227 3.3033 -- 160 2785 0.2266 0.2845 -- 96.0
X Ray Diffraction 3.3033 3.3926 -- 163 2730 0.2236 0.2631 -- 96.0
X Ray Diffraction 3.3926 3.4923 -- 156 2665 0.2173 0.3005 -- 94.0
X Ray Diffraction 3.4923 3.605 -- 154 2793 0.2035 0.3048 -- 97.0
X Ray Diffraction 3.605 3.7337 -- 145 2732 0.1832 0.255 -- 95.0
X Ray Diffraction 3.7337 3.8831 -- 144 2720 0.1782 0.2343 -- 96.0
X Ray Diffraction 3.8831 4.0596 -- 159 2767 0.1555 0.2187 -- 95.0
X Ray Diffraction 4.0596 4.2734 -- 141 2833 0.1442 0.1774 -- 98.0
X Ray Diffraction 4.2734 4.5408 -- 148 2757 0.1395 0.1918 -- 98.0
X Ray Diffraction 4.5408 4.8907 -- 142 2810 0.1466 0.1711 -- 98.0
X Ray Diffraction 4.8907 5.3817 -- 145 2801 0.161 0.2041 -- 97.0
X Ray Diffraction 5.3817 6.1578 -- 149 2753 0.1816 0.2207 -- 96.0
X Ray Diffraction 6.1578 7.7478 -- 158 2795 0.1903 0.2356 -- 97.0
X Ray Diffraction 7.7478 38.6261 -- 141 2593 0.2101 0.2576 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 60.0349
Anisotropic B[1][1] 4.4844
Anisotropic B[1][2] 4.0547
Anisotropic B[1][3] 2.8808
Anisotropic B[2][2] 0.2494
Anisotropic B[2][3] -0.0586
Anisotropic B[3][3] -4.7338
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.08
f_dihedral_angle_d 16.771
f_angle_d 1.162
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14788
Nucleic Acid Atoms 3014
Heterogen Atoms 68
Solvent Atoms 759

Software

Computing
Computing Package Purpose
BLUE-ICE Data Collection
d*TREK Data Reduction (intensity integration)
d*TREK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
PHASER model building
BLUE-ICE data collection