X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.7
Temperature 293.0
Details 0.1 M sodium citrate/citric acid buffer, pH 5.7, 1.5 M lithium chloride, 18%-21% PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.8 α = 90
b = 93.1 β = 90
c = 100.2 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 ADSC QUANTUM 315r -- 2013-07-18
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock double crystal sagittal focusing Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 0.979 NSLS X29A

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
1.9 50 100.0 0.069 -- -- 3.8 129493 129493 2.0 2.0 --
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)
1.9 1.97 100.0 0.439 -- 3.4 3.8 --

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
SAD 1.9 39.682 -- 1.34 128927 128927 6371 99.69 -- 0.1791 0.1774 0.212 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 1.9 1.9679 -- 650 12267 0.2266 0.2652 -- 100.0
X Ray Diffraction 1.9679 2.0467 -- 616 12346 0.1989 0.2381 -- 100.0
X Ray Diffraction 2.0467 2.1398 -- 617 12288 0.1824 0.2298 -- 100.0
X Ray Diffraction 2.1398 2.2526 -- 616 12360 0.175 0.2115 -- 100.0
X Ray Diffraction 2.2526 2.3938 -- 664 12228 0.1744 0.2274 -- 100.0
X Ray Diffraction 2.3938 2.5786 -- 604 12358 0.174 0.2128 -- 100.0
X Ray Diffraction 2.5786 2.838 -- 692 12218 0.1878 0.2104 -- 100.0
X Ray Diffraction 2.838 3.2485 -- 662 12275 0.1863 0.2362 -- 100.0
X Ray Diffraction 3.2485 4.0921 -- 606 12265 0.1599 0.1906 -- 100.0
X Ray Diffraction 4.0921 39.6903 -- 644 11951 0.1715 0.1916 -- 97.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.077
f_dihedral_angle_d 13.772
f_angle_d 1.209
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4741
Nucleic Acid Atoms 767
Heterogen Atoms 20
Solvent Atoms 885

Software

Computing
Computing Package Purpose
CBASS Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHELXD Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.2_1309) refinement
SHELXD model building
CBASS data collection