X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.75
Temperature 291.0
Details 23% PEG 4000, 0.1 M SODIUM ACETATE PH 4.75, 0.2 M AMMONIUM ACETATE, vapor diffusion, hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.81 α = 90
b = 88.77 β = 90
c = 176.12 γ = 90
Symmetry
Space Group P 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M DCM Si(311) and Si(111) 2010-09-09
Diffraction Radiation
Monochromator Protocol
SI(311) AND SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.97627 ESRF ID29

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
1.7 50 98.8 0.051 -- -- -- 77204 76251 2.0 -3.0 34.02
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)
1.696 1.8 98.1 0.59 -- 2.04 -- --

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 1.696 48.967 -- 2.02 77204 76249 3813 98.77 -- 0.1828 0.1814 0.2079 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 1.696 1.7177 -- 129 2454 0.3052 0.3374 -- 93.0
X Ray Diffraction 1.7177 1.7403 -- 143 2717 0.2979 0.3697 -- 100.0
X Ray Diffraction 1.7403 1.7641 -- 139 2646 0.2791 0.3005 -- 100.0
X Ray Diffraction 1.7641 1.7893 -- 139 2639 0.2716 0.2931 -- 100.0
X Ray Diffraction 1.7893 1.816 -- 142 2701 0.2648 0.2947 -- 100.0
X Ray Diffraction 1.816 1.8444 -- 140 2656 0.2584 0.2982 -- 100.0
X Ray Diffraction 1.8444 1.8746 -- 139 2637 0.2399 0.2784 -- 99.0
X Ray Diffraction 1.8746 1.907 -- 144 2744 0.2246 0.2297 -- 100.0
X Ray Diffraction 1.907 1.9416 -- 139 2639 0.201 0.2397 -- 100.0
X Ray Diffraction 1.9416 1.979 -- 143 2705 0.1988 0.2294 -- 100.0
X Ray Diffraction 1.979 2.0194 -- 140 2659 0.1961 0.2285 -- 100.0
X Ray Diffraction 2.0194 2.0633 -- 141 2683 0.1866 0.2127 -- 100.0
X Ray Diffraction 2.0633 2.1113 -- 141 2679 0.1868 0.2002 -- 99.0
X Ray Diffraction 2.1113 2.1641 -- 139 2647 0.1736 0.2001 -- 99.0
X Ray Diffraction 2.1641 2.2226 -- 140 2658 0.176 0.208 -- 99.0
X Ray Diffraction 2.2226 2.288 -- 141 2670 0.1803 0.2453 -- 98.0
X Ray Diffraction 2.288 2.3619 -- 140 2668 0.1787 0.2088 -- 99.0
X Ray Diffraction 2.3619 2.4463 -- 143 2706 0.1771 0.2134 -- 99.0
X Ray Diffraction 2.4463 2.5442 -- 140 2663 0.1764 0.2088 -- 99.0
X Ray Diffraction 2.5442 2.66 -- 141 2680 0.1742 0.2189 -- 99.0
X Ray Diffraction 2.66 2.8002 -- 141 2687 0.1829 0.2217 -- 99.0
X Ray Diffraction 2.8002 2.9756 -- 142 2688 0.1794 0.2176 -- 98.0
X Ray Diffraction 2.9756 3.2053 -- 141 2696 0.1864 0.2251 -- 98.0
X Ray Diffraction 3.2053 3.5278 -- 144 2720 0.1831 0.2039 -- 98.0
X Ray Diffraction 3.5278 4.0381 -- 144 2749 0.1596 0.1837 -- 98.0
X Ray Diffraction 4.0381 5.0867 -- 144 2730 0.1383 0.1446 -- 98.0
X Ray Diffraction 5.0867 48.9875 -- 154 2915 0.1761 0.1886 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.7992
Anisotropic B[1][1] -1.8126
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.0555
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.2429
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.15
f_plane_restr 0.004
f_chiral_restr 0.064
f_angle_d 1.297
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4542
Nucleic Acid Atoms 0
Heterogen Atoms 130
Solvent Atoms 568

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
DM density modification
Phaser molecular replacement
Xscale data reduction