X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 292.0
Details 0.1M Ammonium acetate, 0.05M Tris-HCl pH 8.5, 2.5% PEG-20K, 4-6% MPD, 5.0mM Mg acetate, 2.0mM TCEP, vapor diffusion, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 297.75 α = 90
b = 297.75 β = 90
c = 485.16 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR ADSC QUANTUM 315 -- 2011-07-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97949 APS 24-ID-C

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
7.03 80 99.8 -- -- -- 9.6 39353 38696 -- -3.0 551.17

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 7.0305 77.529 -- 1.34 39353 38696 1941 98.33 -- 0.3454 0.345 0.3592 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 7.0305 7.2062 -- 123 2183 0.4163 0.4019 -- 83.0
X Ray Diffraction 7.2062 7.4009 -- 154 2598 0.4008 0.3809 -- 99.0
X Ray Diffraction 7.4009 7.6185 -- 132 2642 0.3979 0.4365 -- 100.0
X Ray Diffraction 7.6185 7.8642 -- 149 2609 0.3889 0.4434 -- 100.0
X Ray Diffraction 7.8642 8.145 -- 135 2633 0.408 0.4118 -- 100.0
X Ray Diffraction 8.145 8.4707 -- 127 2650 0.3857 0.4906 -- 100.0
X Ray Diffraction 8.4707 8.8557 -- 137 2655 0.383 0.4046 -- 100.0
X Ray Diffraction 8.8557 9.3219 -- 123 2685 0.3806 0.4379 -- 100.0
X Ray Diffraction 9.3219 9.9048 -- 136 2652 0.3829 0.3592 -- 100.0
X Ray Diffraction 9.9048 10.6678 -- 130 2676 0.3655 0.3128 -- 100.0
X Ray Diffraction 10.6678 11.738 -- 153 2650 0.3518 0.3656 -- 100.0
X Ray Diffraction 11.738 13.4289 -- 143 2690 0.3422 0.3585 -- 100.0
X Ray Diffraction 13.4289 16.8902 -- 162 2707 0.3666 0.3938 -- 100.0
X Ray Diffraction 16.8902 77.5335 -- 137 2725 0.3023 0.318 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 179.892
Anisotropic B[1][1] 583.846
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 583.846
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 498.253
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.567
f_plane_restr 0.022
f_chiral_restr 0.238
f_angle_d 2.743
f_bond_d 0.026
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 39654
Nucleic Acid Atoms 39394
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
xds Data Reduction (intensity integration)
xds Data Reduction (data scaling)
phaser Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement