X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 291.0
Details 0.8-1.0 M lithium sulfate, 0.075-0.2 M potassium iodide, 0.05-0.2 M trisodium citrate, pH 5-6

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 141.23 α = 90
b = 141.23 β = 90
c = 174.48 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2014-09-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.280 NSLS X25

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
2.6 100 100.0 0.046 -- -- 9.3 -- 59600 -- -- 66.39
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)
2.6 2.62 -- 0.597 -- -- -- --

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
SAD 2.614 61.155 -- 1.92 -- 59520 3006 99.91 -- 0.2317 0.2305 0.255 --
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 2.6135 2.6564 -- 138 2649 0.3064 0.3318 0.0 99.0
X Ray Diffraction 2.6564 2.7022 -- 133 2702 0.2935 0.2887 0.0 100.0
X Ray Diffraction 2.7022 2.7513 -- 146 2645 0.287 0.303 0.0 100.0
X Ray Diffraction 2.7513 2.8042 -- 144 2699 0.2804 0.3191 0.0 100.0
X Ray Diffraction 2.8042 2.8615 -- 140 2680 0.289 0.3161 0.0 100.0
X Ray Diffraction 2.8615 2.9237 -- 140 2698 0.3144 0.2976 0.0 100.0
X Ray Diffraction 2.9237 2.9917 -- 138 2708 0.3051 0.3843 0.0 100.0
X Ray Diffraction 2.9917 3.0665 -- 149 2677 0.3049 0.3106 0.0 100.0
X Ray Diffraction 3.0665 3.1494 -- 128 2678 0.2847 0.3647 0.0 100.0
X Ray Diffraction 3.1494 3.2421 -- 168 2659 0.2776 0.2867 0.0 100.0
X Ray Diffraction 3.2421 3.3467 -- 147 2703 0.2658 0.2816 0.0 100.0
X Ray Diffraction 3.3467 3.4663 -- 142 2667 0.2587 0.2714 0.0 100.0
X Ray Diffraction 3.4663 3.6051 -- 150 2706 0.2537 0.2519 0.0 100.0
X Ray Diffraction 3.6051 3.7692 -- 149 2679 0.2379 0.2541 0.0 100.0
X Ray Diffraction 3.7692 3.9678 -- 139 2695 0.2107 0.2377 0.0 100.0
X Ray Diffraction 3.9678 4.2164 -- 141 2703 0.2023 0.2233 0.0 100.0
X Ray Diffraction 4.2164 4.5418 -- 149 2700 0.1895 0.2223 0.0 100.0
X Ray Diffraction 4.5418 4.9987 -- 139 2711 0.1833 0.2257 0.0 100.0
X Ray Diffraction 4.9987 5.7216 -- 132 2707 0.2062 0.2258 0.0 100.0
X Ray Diffraction 5.7216 7.2068 -- 146 2713 0.2401 0.2442 0.0 100.0
X Ray Diffraction 7.2068 61.172 -- 148 2735 0.2036 0.2414 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 95.1683
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_bond_d 0.003
f_angle_d 0.603
f_dihedral_angle_d 12.606
f_chiral_restr 0.042
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8361
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 22

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10_2155
Aimless data scaling
PDB_EXTRACT data extraction version: 3.22
XDS data reduction
PHENIX phasing