X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 0.1 M Bicine, pH 7.5, 0.75 M lithium chloride, 6% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 152.7 α = 90
b = 152.7 β = 90
c = 129.5 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2011-08-11
PIXEL DECTRIS PILATUS 6M -- 2011-07-11
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 0.9793 SLS X10SA
SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA

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
2.8 49.83 100.0 0.081 -- -- 13.29 38042 38042 0.0 -3.0 66.273
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)
2.8 2.87 100.0 0.737 -- 3.51 -- --

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 2.804 49.831 -3.0 2.02 -- 38034 1902 99.83 -- 0.2015 0.1995 0.238 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 2.804 2.8746 -- 130 2500 0.2414 0.3009 -- 98.0
X Ray Diffraction 2.8746 2.9523 -- 133 2529 0.2397 0.2673 -- 100.0
X Ray Diffraction 2.9523 3.0392 -- 136 2550 0.2391 0.2832 -- 100.0
X Ray Diffraction 3.0392 3.1373 -- 134 2540 0.2311 0.2886 -- 100.0
X Ray Diffraction 3.1373 3.2494 -- 135 2553 0.2442 0.2782 -- 100.0
X Ray Diffraction 3.2494 3.3794 -- 133 2545 0.2249 0.2839 -- 100.0
X Ray Diffraction 3.3794 3.5332 -- 134 2551 0.2113 0.2292 -- 100.0
X Ray Diffraction 3.5332 3.7194 -- 135 2577 0.2063 0.257 -- 100.0
X Ray Diffraction 3.7194 3.9524 -- 135 2563 0.1903 0.2243 -- 100.0
X Ray Diffraction 3.9524 4.2574 -- 136 2577 0.182 0.237 -- 100.0
X Ray Diffraction 4.2574 4.6855 -- 136 2598 0.1743 0.2151 -- 100.0
X Ray Diffraction 4.6855 5.3629 -- 139 2613 0.185 0.2305 -- 100.0
X Ray Diffraction 5.3629 6.754 -- 138 2648 0.2211 0.2516 -- 100.0
X Ray Diffraction 6.754 49.8386 -- 148 2788 0.1794 0.205 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 76.5663
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.172
f_plane_restr 0.003
f_chiral_restr 0.051
f_angle_d 0.676
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6483
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 28

Software

Computing
Computing Package Purpose
XDS Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
SOLVE Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SOLVE version: 2.13 phasing
Xscale data reduction