X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.0
Details 100mM Bis-tris pH 6.1-6.7, 200mM LiSO4, 16-20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.97 α = 90
b = 180.12 β = 90
c = 79.27 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r Compound Refractive Lenses 2011-09-25
Diffraction Radiation
Monochromator Protocol
DCM SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 0.96110 DIAMOND I04

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
2.26 90.06 97.4 0.099 -- -- -- 40098 40098 -3.0 -3.0 36.926
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)
2.26 2.32 97.4 0.57 -- 1.63 -- --

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 2.26 90.06 -- 1.34 40098 40098 2011 99.17 -- 0.1792 0.1771 0.2216 --
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 2.26 2.3165 -- 130 2650 0.2376 0.2791 -- 99.0
X Ray Diffraction 2.3165 2.3792 -- 143 2662 0.2219 0.289 -- 99.0
X Ray Diffraction 2.3792 2.4492 -- 146 2704 0.2123 0.2788 -- 99.0
X Ray Diffraction 2.4492 2.5283 -- 136 2683 0.2021 0.2406 -- 99.0
X Ray Diffraction 2.5283 2.6186 -- 172 2624 0.1886 0.2404 -- 99.0
X Ray Diffraction 2.6186 2.7235 -- 149 2710 0.1833 0.2256 -- 99.0
X Ray Diffraction 2.7235 2.8474 -- 139 2691 0.1895 0.2446 -- 99.0
X Ray Diffraction 2.8474 2.9976 -- 144 2706 0.1956 0.2675 -- 99.0
X Ray Diffraction 2.9976 3.1854 -- 127 2728 0.1949 0.2717 -- 99.0
X Ray Diffraction 3.1854 3.4313 -- 142 2736 0.1778 0.2405 -- 100.0
X Ray Diffraction 3.4313 3.7766 -- 152 2722 0.1594 0.1921 -- 99.0
X Ray Diffraction 3.7766 4.3231 -- 141 2751 0.1518 0.1695 -- 99.0
X Ray Diffraction 4.3231 5.4466 -- 151 2787 0.141 0.1844 -- 99.0
X Ray Diffraction 5.4466 90.1315 -- 139 2933 0.1834 0.2207 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.0587
Anisotropic B[1][1] -7.6289
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 9.2205
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.19
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.058
f_dihedral_angle_d 12.814
f_angle_d 0.819
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5354
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 278

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Xscale data reduction