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 = 296.9 α = 90
b = 296.9 β = 90
c = 478.3 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 -- 2012-06-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9789 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
7.01 120 99.7 -- -- -- -- 39111 38929 -- -3.0 464.07

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 7.01 113.236 -- 1.34 39111 38188 1921 98.03 0.3653 0.3653 0.3662 0.3478 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 7.0103 7.1856 -- 121 2133 0.507 0.4781 -- 81.0
X Ray Diffraction 7.1856 7.3799 -- 121 2548 0.4689 0.4718 -- 98.0
X Ray Diffraction 7.3799 7.597 -- 141 2564 0.4393 0.4291 -- 98.0
X Ray Diffraction 7.597 7.8421 -- 150 2563 0.4321 0.4002 -- 99.0
X Ray Diffraction 7.8421 8.1223 -- 138 2576 0.4205 0.4436 -- 99.0
X Ray Diffraction 8.1223 8.4474 -- 137 2626 0.4195 0.3579 -- 100.0
X Ray Diffraction 8.4474 8.8318 -- 134 2614 0.4075 0.4208 -- 100.0
X Ray Diffraction 8.8318 9.2972 -- 126 2639 0.4235 0.3822 -- 100.0
X Ray Diffraction 9.2972 9.8794 -- 134 2639 0.4153 0.4026 -- 100.0
X Ray Diffraction 9.8794 10.6416 -- 152 2609 0.3909 0.4058 -- 100.0
X Ray Diffraction 10.6416 11.7116 -- 126 2668 0.387 0.3724 -- 100.0
X Ray Diffraction 11.7116 13.4039 -- 149 2631 0.372 0.3348 -- 100.0
X Ray Diffraction 13.4039 16.8785 -- 142 2669 0.388 0.3766 -- 99.0
X Ray Diffraction 16.8785 113.251 -- 150 2788 0.308 0.2842 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 235.354
Anisotropic B[1][1] 582.563
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 582.563
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 371.495
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.723
f_plane_restr 0.022
f_chiral_restr 0.24
f_angle_d 2.784
f_bond_d 0.026
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 40341
Nucleic Acid Atoms 38071
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