X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.3
Temperature 294.0
Details 15% PEG 3350, 0.05M magnesium chloride, 0.067M sodium chloride, 0.1M Tris, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.75 α = 90
b = 81.54 β = 109.87
c = 58.45 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
PIXEL DECTRIS PILATUS 6M -- 2012-07-27
Diffraction Radiation
Monochromator Protocol
Side scattering bent cube I-beam single crystal, asymmetric cut 4.965 degs SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 1.0 SSRL BL11-1

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
1.95 50 96.45 -- 0.088 -- 6.5 34396 34396 1.0 1.0 30.79
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)
1.95 1.98 88.83 -- 0.869 2.17 6.6 --

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 1.95 46.226 -- 0.0 32363 32363 1861 90.75 0.2121 0.2121 0.2109 0.2322 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 1.95 1.9956 -- 105 1859 0.2728 0.3156 -- 72.0
X Ray Diffraction 1.9956 2.0544 -- 144 2194 0.2598 0.3103 -- 86.0
X Ray Diffraction 2.0544 2.1207 -- 143 2276 0.2408 0.2944 -- 89.0
X Ray Diffraction 2.1207 2.1965 -- 124 2313 0.2282 0.2526 -- 89.0
X Ray Diffraction 2.1965 2.2844 -- 131 2124 0.2663 0.2939 -- 82.0
X Ray Diffraction 2.2844 2.3884 -- 142 2425 0.2195 0.2562 -- 94.0
X Ray Diffraction 2.3884 2.5143 -- 158 2482 0.2159 0.2551 -- 96.0
X Ray Diffraction 2.5143 2.6718 -- 152 2462 0.2158 0.29 -- 96.0
X Ray Diffraction 2.6718 2.8781 -- 154 2450 0.2208 0.2306 -- 95.0
X Ray Diffraction 2.8781 3.1676 -- 151 2543 0.2196 0.2216 -- 98.0
X Ray Diffraction 3.1676 3.6258 -- 151 2461 0.2066 0.2305 -- 95.0
X Ray Diffraction 3.6258 4.5675 -- 149 2334 0.1779 0.2062 -- 90.0
X Ray Diffraction 4.5675 46.226 -- 157 2579 0.2009 0.1947 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.1807
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 4.353
Anisotropic B[2][2] 3.622
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.4413
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.001
f_chiral_restr 0.037
f_dihedral_angle_d 14.006
f_angle_d 0.528
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3813
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 222

Software

Computing
Computing Package Purpose
Blue ice Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX (phenix.automr) Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
PHENIX version: (phenix.automr) model building
Blue version: ice data collection