X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details 1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.69 α = 90
b = 107.69 β = 90
c = 90.77 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Radiation
Monochromator Protocol
-- --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E

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
2.05 50 99.9 -- -- -- -- 33889 33889 2.0 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 2.053 38.075 4.2 1.36 33826 33826 1710 99.74 0.2245 0.1843 0.1822 0.2245 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 2.053 2.1135 -- 154 2563 0.2285 0.2819 -- 98.0
X Ray Diffraction 2.1135 2.1817 -- 143 2617 0.2117 0.2656 -- 100.0
X Ray Diffraction 2.1817 2.2597 -- 134 2645 0.2017 0.2445 -- 100.0
X Ray Diffraction 2.2597 2.3501 -- 153 2640 0.2092 0.255 -- 100.0
X Ray Diffraction 2.3501 2.4571 -- 130 2666 0.1951 0.2638 -- 100.0
X Ray Diffraction 2.4571 2.5866 -- 152 2619 0.2013 0.2558 -- 100.0
X Ray Diffraction 2.5866 2.7486 -- 153 2665 0.1988 0.2315 -- 100.0
X Ray Diffraction 2.7486 2.9608 -- 129 2683 0.1878 0.237 -- 100.0
X Ray Diffraction 2.9608 3.2586 -- 127 2706 0.1896 0.2464 -- 100.0
X Ray Diffraction 3.2586 3.7297 -- 141 2699 0.174 0.1957 -- 100.0
X Ray Diffraction 3.7297 4.6977 -- 154 2743 0.1462 0.1785 -- 100.0
X Ray Diffraction 4.6977 38.075 -- 140 2870 0.1844 0.2347 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -4.596
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.596
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 9.1921
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.067
f_dihedral_angle_d 15.322
f_angle_d 1.005
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3086
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 224

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.2_869) refinement
PHASER model building
HKL-2000 data collection