X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 298.0
Details 30% PEG 3350, 100 mM NaAcetate, 100 mM Tris pH 8.5, 0.1 mM TCEP, 20% ethylene glycol, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.22 α = 90
b = 107.7 β = 100.2
c = 86.14 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2009-09-17
Diffraction Radiation
Monochromator Protocol
Double silicon(111) crystal Single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 0.98 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
2.4 50 100.0 0.138 -- -- 8.3 -- 44580 -- -- --
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)
2.4 2.44 100.0 0.706 -- -- 8.4 2236

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 2.4 42.609 -- 1.35 -- 44511 2242 99.75 -- 0.1941 0.1915 0.241 --
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 2.4 2.4824 -- 218 4122 0.2328 0.3141 -- 99.0
X Ray Diffraction 2.4824 2.5818 -- 229 4234 0.2201 0.2574 -- 100.0
X Ray Diffraction 2.5818 2.6992 -- 210 4254 0.2204 0.282 -- 100.0
X Ray Diffraction 2.6992 2.8415 -- 201 4232 0.2264 0.3206 -- 100.0
X Ray Diffraction 2.8415 3.0195 -- 236 4206 0.2252 0.2955 -- 100.0
X Ray Diffraction 3.0195 3.2526 -- 232 4206 0.1985 0.2613 -- 100.0
X Ray Diffraction 3.2526 3.5797 -- 223 4253 0.1718 0.2345 -- 100.0
X Ray Diffraction 3.5797 4.0974 -- 216 4217 0.1625 0.2053 -- 100.0
X Ray Diffraction 4.0974 5.1608 -- 234 4260 0.1422 0.186 -- 100.0
X Ray Diffraction 5.1608 42.6162 -- 243 4285 0.1624 0.1926 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.691
Anisotropic B[1][1] 8.1853
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.4908
Anisotropic B[2][2] -10.5909
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.4056
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 21.43
f_plane_restr 0.005
f_chiral_restr 0.072
f_angle_d 1.269
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5697
Nucleic Acid Atoms 1616
Heterogen Atoms 8
Solvent Atoms 342

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SHELXS Structure Solution
PHENIX (phenix.refine: 1.6.1_357) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
HKL data processing