X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 298.0
Details 100 mM sodium citrate, 30% PEG 2000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 33.57 α = 90
b = 40.46 β = 90
c = 75.84 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2013-04-20
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 0.9792 APS 21-ID-D

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
1.5 22.1 99.5 0.054 -- 33.32 6.1 -- 17064 -- -- 17.96
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)
1.5 1.55 98.5 0.419 -- -- 6.1 1653

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 1.502 21.439 -- 1.36 -- 17020 1703 99.46 -- 0.174 0.1705 0.2058 random selection
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 1.502 1.5458 -- 135 1214 0.1944 0.2418 -- 97.0
X Ray Diffraction 1.5458 1.5956 -- 141 1277 0.1805 0.2246 -- 99.0
X Ray Diffraction 1.5956 1.6526 -- 138 1228 0.1644 0.1798 -- 100.0
X Ray Diffraction 1.6526 1.7188 -- 137 1239 0.1818 0.2278 -- 99.0
X Ray Diffraction 1.7188 1.797 -- 140 1259 0.172 0.2015 -- 99.0
X Ray Diffraction 1.797 1.8917 -- 139 1262 0.1744 0.222 -- 100.0
X Ray Diffraction 1.8917 2.0101 -- 143 1283 0.1614 0.2118 -- 100.0
X Ray Diffraction 2.0101 2.1652 -- 142 1269 0.1651 0.1962 -- 100.0
X Ray Diffraction 2.1652 2.3828 -- 144 1301 0.1709 0.2023 -- 100.0
X Ray Diffraction 2.3828 2.727 -- 142 1282 0.1773 0.2245 -- 100.0
X Ray Diffraction 2.727 3.4335 -- 147 1313 0.1737 0.2159 -- 100.0
X Ray Diffraction 3.4335 21.4412 -- 155 1390 0.1651 0.1893 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.3415
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_dihedral_angle_d 14.485
f_angle_d 1.181
f_chiral_restr 0.081
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 797
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 90

Software

Software
Software Name Purpose
PHENIX refinement version: 1.8.1_1168
DENZO data reduction
PDB_EXTRACT data extraction version: 3.14
SCALEPACK data scaling
PHASER phasing