X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Details Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.87 α = 90
b = 40.88 β = 106.49
c = 82.4 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 MAR CCD 165 mm mirrors 2011-04-14
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4C 0.979 NSLS X4C

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
2.6 39.09 94.7 0.112 -- -- 5.4 -- 28693 -- -3.0 --

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
SAD 2.604 39.086 -- 0.13 -- 14803 1574 92.3 -- 0.2367 0.2326 0.2976 --
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 2.6067 2.6908 -- 92 817 0.2827 0.3678 -- 56.0
X Ray Diffraction 2.6908 2.7869 -- 121 1034 0.2723 0.3707 -- 72.0
X Ray Diffraction 2.7869 2.8984 -- 127 1184 0.2611 0.3219 -- 82.0
X Ray Diffraction 2.8984 3.0303 -- 134 1200 0.2645 0.3526 -- 85.0
X Ray Diffraction 3.0303 3.1899 -- 144 1249 0.2569 0.2924 -- 86.0
X Ray Diffraction 3.1899 3.3896 -- 140 1280 0.2377 0.3164 -- 88.0
X Ray Diffraction 3.3896 3.6511 -- 152 1262 0.2325 0.3015 -- 88.0
X Ray Diffraction 3.6511 4.018 -- 146 1293 0.2112 0.281 -- 89.0
X Ray Diffraction 4.018 4.5983 -- 144 1305 0.2062 0.2267 -- 89.0
X Ray Diffraction 4.5983 5.789 -- 150 1311 0.2134 0.287 -- 89.0
X Ray Diffraction 5.789 34.6058 -- 152 1359 0.2188 0.3069 -- 89.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.825
Anisotropic B[1][1] -7.206
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -6.274
Anisotropic B[2][2] 1.742
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.464
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.076
f_dihedral_angle_d 16.232
f_angle_d 1.189
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2862
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 41

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
Phenix (AutoSolve) Structure Solution
PHENIX (phenix.refine: dev_1269) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.100 data extraction
phenix refinement