X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 293.0
Details 20% w/v PEG3350, 0.2 M lithium citrate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 172.44 α = 90
b = 172.44 β = 90
c = 92.43 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2012-04-12
Diffraction Radiation
Monochromator Protocol
Double crystal cryo-cooled Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.03320 APS 23-ID-B

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
2.1 86.22 100.0 -- 0.086 -- 5.8 59819 59809 0.0 0.0 30.03
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)
2.1 2.2 100.0 -- 0.521 2.8 5.8 --

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 2.1 44.149 -- 0.1 -- 58400 2914 97.64 -- 0.1766 0.1747 0.2143 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 2.1 2.1345 -- 131 2551 0.2524 0.2981 -- 94.0
X Ray Diffraction 2.1345 2.1713 -- 136 2573 0.2489 0.3065 -- 95.0
X Ray Diffraction 2.1713 2.2107 -- 129 2548 0.2278 0.2586 -- 94.0
X Ray Diffraction 2.2107 2.2533 -- 139 2565 0.2333 0.2737 -- 96.0
X Ray Diffraction 2.2533 2.2993 -- 142 2596 0.2305 0.2863 -- 96.0
X Ray Diffraction 2.2993 2.3492 -- 132 2595 0.2269 0.2286 -- 96.0
X Ray Diffraction 2.3492 2.4039 -- 138 2612 0.2303 0.3251 -- 97.0
X Ray Diffraction 2.4039 2.464 -- 135 2598 0.2298 0.3068 -- 96.0
X Ray Diffraction 2.464 2.5306 -- 141 2649 0.2196 0.2806 -- 97.0
X Ray Diffraction 2.5306 2.6051 -- 145 2655 0.2185 0.2946 -- 98.0
X Ray Diffraction 2.6051 2.6891 -- 139 2635 0.2067 0.264 -- 98.0
X Ray Diffraction 2.6891 2.7852 -- 140 2653 0.2025 0.2371 -- 98.0
X Ray Diffraction 2.7852 2.8967 -- 140 2664 0.1951 0.2459 -- 99.0
X Ray Diffraction 2.8967 3.0286 -- 140 2673 0.1795 0.2285 -- 99.0
X Ray Diffraction 3.0286 3.1882 -- 139 2703 0.1728 0.2181 -- 99.0
X Ray Diffraction 3.1882 3.3879 -- 137 2675 0.1631 0.1927 -- 100.0
X Ray Diffraction 3.3879 3.6493 -- 143 2727 0.1452 0.1839 -- 100.0
X Ray Diffraction 3.6493 4.0163 -- 141 2713 0.1452 0.2028 -- 100.0
X Ray Diffraction 4.0163 4.597 -- 144 2689 0.1242 0.157 -- 100.0
X Ray Diffraction 4.597 5.7897 -- 142 2711 0.1384 0.1574 -- 100.0
X Ray Diffraction 5.7897 44.159 -- 141 2701 0.1668 0.1753 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.283
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.105
f_bond_d 0.007
f_plane_restr 0.005
f_dihedral_angle_d 14.563
f_chiral_restr 0.078
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6488
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 387

Software

Software
Software Name Purpose
JBluIce-EPICS data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.8.1_1168)
XDS data reduction
XDS data scaling