X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 298.0
Details 0.2 M magnesium chloride, 0.1 M MES/NaOH, pH 6.0, 27.5% PEG3350, 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.95 α = 90
b = 80.82 β = 90
c = 126.04 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- --
Diffraction Radiation
Monochromator Protocol
ACCEL/BRUKER double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1

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
1.6 47.1 -- -- -- -- -- -- 38225 -- -- 18.12
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)
1.6 1.65 78.8 -- -- -- -- --

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 1.6 47.095 -- 1.36 -- 38225 1912 97.01 -- 0.1609 0.1589 0.1987 --
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 1.6 1.64 -- 106 2017 0.1825 0.2482 -- 77.0
X Ray Diffraction 1.64 1.6844 -- 121 2301 0.1918 0.2413 -- 87.0
X Ray Diffraction 1.6844 1.7339 -- 133 2511 0.1787 0.2336 -- 95.0
X Ray Diffraction 1.7339 1.7899 -- 139 2647 0.1783 0.2522 -- 100.0
X Ray Diffraction 1.7899 1.8539 -- 138 2631 0.1708 0.2218 -- 100.0
X Ray Diffraction 1.8539 1.9281 -- 141 2663 0.1751 0.2168 -- 99.0
X Ray Diffraction 1.9281 2.0159 -- 138 2626 0.1622 0.2021 -- 100.0
X Ray Diffraction 2.0159 2.1222 -- 140 2652 0.1568 0.2128 -- 100.0
X Ray Diffraction 2.1222 2.2551 -- 140 2679 0.1583 0.186 -- 100.0
X Ray Diffraction 2.2551 2.4292 -- 140 2650 0.1644 0.2322 -- 100.0
X Ray Diffraction 2.4292 2.6737 -- 141 2682 0.168 0.1865 -- 100.0
X Ray Diffraction 2.6737 3.0605 -- 142 2700 0.1657 0.2158 -- 100.0
X Ray Diffraction 3.0605 3.8556 -- 144 2729 0.1469 0.1814 -- 100.0
X Ray Diffraction 3.8556 47.1151 -- 149 2825 0.1444 0.1683 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.093
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.012
f_chiral_restr 0.091
f_dihedral_angle_d 14.102
f_angle_d 1.635
f_plane_restr 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2473
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 425

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHENIX refinement version: 1.8.4_1496
PDB_EXTRACT data extraction version: 3.15