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 = 292.12 α = 90
b = 292.12 β = 90
c = 477.67 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
PIXEL DECTRIS PILATUS 6M -- 2011-07-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25

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
9 80 99.3 -- -- -- -- 18057 17938 -- -3.0 667.15

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 7.809 58.112 -- 1.33 27341 25914 1304 94.78 -- 0.3469 0.3469 0.3471 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 7.809 8.1209 -- 87 1676 0.4443 0.4356 -- 58.0
X Ray Diffraction 8.1209 8.4894 -- 134 2764 0.4199 0.4597 -- 98.0
X Ray Diffraction 8.4894 8.9355 -- 146 2822 0.4027 0.4322 -- 100.0
X Ray Diffraction 8.9355 9.4931 -- 141 2867 0.3912 0.4186 -- 100.0
X Ray Diffraction 9.4931 10.2224 -- 156 2851 0.3863 0.4208 -- 100.0
X Ray Diffraction 10.2224 11.2444 -- 179 2857 0.3512 0.3509 -- 100.0
X Ray Diffraction 11.2444 12.8562 -- 165 2862 0.3582 0.3308 -- 100.0
X Ray Diffraction 12.8562 16.1397 -- 148 2926 0.3608 0.3838 -- 100.0
X Ray Diffraction 16.1397 58.1134 -- 148 2985 0.3096 0.2971 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 216.999
Anisotropic B[1][1] 669.983
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 669.983
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 411.798
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.69
f_plane_restr 0.022
f_chiral_restr 0.24
f_angle_d 2.813
f_bond_d 0.026
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 39697
Nucleic Acid Atoms 37514
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
CBASS 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