X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.15
Details 50 mM Na cacodylate, 1 mM spermine tetrahydrochloride, 1-20% 2-methyl-2,4-pentadiol (vs. 40% reservoir), 100-200 mM KCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 33.08 α = 90
b = 90.76 β = 90
c = 47.01 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 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9394 ESRF ID14-4

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
2.5 50 81.6 0.046 -- -- -- 21134 4294 21.5 21.5 --
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)
2.5 2.57 84.7 0.64 -- 2.0 -- --

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 2.5 23.505 -- 2.04 4290 4290 429 81.64 -- 0.2096 0.2058 0.2445 --
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 2.5004 2.8616 -- 143 1295 0.3186 0.3486 -- 85.0
X Ray Diffraction 2.8616 3.6033 -- 144 1300 0.2102 0.2987 -- 83.0
X Ray Diffraction 3.6033 23.506 -- 142 1266 0.1768 0.1956 -- 77.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.5826
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -7.1484
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.5658
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.006
f_chiral_restr 0.057
f_plane_restr 0.008
f_angle_d 0.954
f_dihedral_angle_d 16.821
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 898
Heterogen Atoms 68
Solvent Atoms 11

Software

Software
Software Name Purpose
DNA data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.6.1_357)
XDS data reduction
XDS data scaling