X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 0.1M TRIS pH 8.0, 1% PEG400, 1.9M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 103.8 α = 90
b = 107.55 β = 90
c = 143.11 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
CCD ADSC Quantum Q315r -- 2012-03-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U

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
2.28 43.61 97.5 0.069 -- -- -- -- 137838 -- -3.0 52.413
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)
2.28 2.42 97.3 0.7 -- 2.0 -- --

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 2.3637 43.606 -- 1.34 -- 64828 3288 97.92 -- 0.2404 0.2373 0.2992 --
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 2.3637 2.399 -- 150 2654 0.3205 0.4108 -- 99.0
X Ray Diffraction 2.399 2.4365 -- 169 2676 0.2947 0.3586 -- 100.0
X Ray Diffraction 2.4365 2.4764 -- 132 2695 0.2876 0.3337 -- 100.0
X Ray Diffraction 2.4764 2.5191 -- 141 2708 0.2797 0.3366 -- 100.0
X Ray Diffraction 2.5191 2.5649 -- 140 2707 0.2578 0.3085 -- 100.0
X Ray Diffraction 2.5649 2.6143 -- 151 2697 0.2811 0.3823 -- 100.0
X Ray Diffraction 2.6143 2.6676 -- 141 2610 0.2996 0.3408 -- 98.0
X Ray Diffraction 2.6676 2.7256 -- 131 2151 0.306 0.4048 -- 80.0
X Ray Diffraction 2.7256 2.789 -- 131 2709 0.3043 0.3803 -- 100.0
X Ray Diffraction 2.789 2.8587 -- 139 2722 0.2814 0.3604 -- 100.0
X Ray Diffraction 2.8587 2.936 -- 157 2694 0.2806 0.3681 -- 100.0
X Ray Diffraction 2.936 3.0224 -- 146 2707 0.2864 0.3393 -- 100.0
X Ray Diffraction 3.0224 3.1199 -- 132 2739 0.2674 0.3617 -- 100.0
X Ray Diffraction 3.1199 3.2314 -- 150 2730 0.2638 0.3004 -- 100.0
X Ray Diffraction 3.2314 3.3607 -- 143 2726 0.2564 0.3252 -- 100.0
X Ray Diffraction 3.3607 3.5136 -- 129 2521 0.2433 0.294 -- 92.0
X Ray Diffraction 3.5136 3.6988 -- 169 2701 0.2612 0.3523 -- 100.0
X Ray Diffraction 3.6988 3.9304 -- 123 2415 0.2325 0.2777 -- 88.0
X Ray Diffraction 3.9304 4.2336 -- 159 2733 0.2033 0.2488 -- 100.0
X Ray Diffraction 4.2336 4.6592 -- 133 2786 0.1801 0.2418 -- 100.0
X Ray Diffraction 4.6592 5.3324 -- 133 2788 0.182 0.2407 -- 100.0
X Ray Diffraction 5.3324 6.7143 -- 147 2813 0.2352 0.2757 -- 100.0
X Ray Diffraction 6.7143 43.613 -- 142 2858 0.1972 0.2364 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.4082
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.091
f_dihedral_angle_d 20.754
f_angle_d 1.395
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10448
Nucleic Acid Atoms 0
Heterogen Atoms 189
Solvent Atoms 84

Software

Computing
Computing Package Purpose
Bluice Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser version: 2.3.0 molecular replacement
Xscale data reduction