X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 289.0
Details 10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.02 M of each carboxylic acid, 0.1 M bicine/Trizma base pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.37 α = 90
b = 136.37 β = 90
c = 364.52 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR scanner 300 mm plate -- 2012-07-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
2.65 50 99.3 0.084 -- -- -- 220240 218698 2.0 2.0 45.565
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)
2.65 2.72 99.6 0.428 -- 2.84 -- --

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 2.65 49.556 -- 0.0 60755 57852 2903 97.89 -- 0.1874 0.1843 0.2468 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 2.65 2.6934 -- 131 2438 0.2007 0.2896 -- 94.0
X Ray Diffraction 2.6934 2.7398 -- 131 2471 0.2094 0.3053 -- 94.0
X Ray Diffraction 2.7398 2.7897 -- 133 2480 0.2148 0.3638 -- 95.0
X Ray Diffraction 2.7897 2.8433 -- 135 2524 0.2036 0.2823 -- 96.0
X Ray Diffraction 2.8433 2.9013 -- 135 2528 0.2037 0.3123 -- 97.0
X Ray Diffraction 2.9013 2.9644 -- 133 2551 0.2193 0.3037 -- 97.0
X Ray Diffraction 2.9644 3.0334 -- 132 2544 0.2109 0.2937 -- 97.0
X Ray Diffraction 3.0334 3.1092 -- 139 2583 0.2088 0.3232 -- 98.0
X Ray Diffraction 3.1092 3.1933 -- 133 2560 0.2014 0.2385 -- 98.0
X Ray Diffraction 3.1933 3.2872 -- 135 2587 0.1918 0.2639 -- 98.0
X Ray Diffraction 3.2872 3.3933 -- 139 2616 0.1971 0.2704 -- 98.0
X Ray Diffraction 3.3933 3.5145 -- 137 2614 0.1944 0.2458 -- 99.0
X Ray Diffraction 3.5145 3.6552 -- 139 2625 0.1909 0.2714 -- 99.0
X Ray Diffraction 3.6552 3.8215 -- 140 2638 0.1719 0.218 -- 99.0
X Ray Diffraction 3.8215 4.0229 -- 141 2675 0.1724 0.2213 -- 100.0
X Ray Diffraction 4.0229 4.2748 -- 142 2678 0.1521 0.2354 -- 100.0
X Ray Diffraction 4.2748 4.6047 -- 141 2677 0.1309 0.1791 -- 100.0
X Ray Diffraction 4.6047 5.0677 -- 143 2711 0.1398 0.1886 -- 100.0
X Ray Diffraction 5.0677 5.8 -- 144 2736 0.1821 0.2315 -- 100.0
X Ray Diffraction 5.8 7.3036 -- 147 2776 0.2121 0.2793 -- 100.0
X Ray Diffraction 7.3036 49.5645 -- 153 2937 0.213 0.227 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.6234
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.043
f_plane_restr 0.007
f_chiral_restr 0.083
f_angle_d 1.552
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9169
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 104

Software

Computing
Computing Package Purpose
HKL-3000 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 molecular replacement
Xscale data reduction