X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 306.0
Details 2.8 M sodium acetate, 0.1 M Bis-Tris propane, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 306K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.92 α = 90
b = 117.42 β = 90
c = 160.46 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-11-15
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.97 SSRF BL17U

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
2.89 50 95.5 0.16 -- -- 4.3 47634 45264 1.0 1.0 42.94
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)
2.89 3.0 82.2 -- -- -- -- --

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 2.89 49.372 -- 1.39 45258 45258 2293 95.05 -- 0.2215 0.219 0.2687 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 2.89 2.9529 -- 108 1952 0.3443 0.398 -- 70.0
X Ray Diffraction 2.9529 3.0216 -- 139 2469 0.3379 0.372 -- 89.0
X Ray Diffraction 3.0216 3.0971 -- 132 2590 0.3168 0.3715 -- 92.0
X Ray Diffraction 3.0971 3.1809 -- 131 2607 0.2771 0.3366 -- 94.0
X Ray Diffraction 3.1809 3.2744 -- 144 2672 0.2591 0.3095 -- 96.0
X Ray Diffraction 3.2744 3.3801 -- 146 2667 0.2426 0.3068 -- 96.0
X Ray Diffraction 3.3801 3.5009 -- 156 2701 0.2186 0.2733 -- 96.0
X Ray Diffraction 3.5009 3.641 -- 164 2684 0.2014 0.267 -- 97.0
X Ray Diffraction 3.641 3.8067 -- 138 2793 0.2048 0.2472 -- 98.0
X Ray Diffraction 3.8067 4.0073 -- 143 2747 0.1778 0.2413 -- 98.0
X Ray Diffraction 4.0073 4.2582 -- 135 2803 0.1649 0.2217 -- 98.0
X Ray Diffraction 4.2582 4.5868 -- 154 2780 0.1603 0.1876 -- 99.0
X Ray Diffraction 4.5868 5.048 -- 151 2816 0.166 0.2168 -- 99.0
X Ray Diffraction 5.048 5.7774 -- 132 2841 0.1992 0.2581 -- 99.0
X Ray Diffraction 5.7774 7.2752 -- 157 2855 0.2393 0.282 -- 99.0
X Ray Diffraction 7.2752 49.3791 -- 163 2988 0.2381 0.2712 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.3682
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.971
f_chiral_restr 0.056
f_plane_restr 0.004
f_angle_d 1.107
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9918
Nucleic Acid Atoms 848
Heterogen Atoms 25
Solvent Atoms 27

Software

Software
Software Name Purpose
PHASER phasing
PHENIX refinement version: 1.8.2_1309
PDB_EXTRACT data extraction version: 3.11
HKL-2000 data collection
DENZO data reduction
SCALEPACK data scaling
HKL-2000 data scaling