X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 295.0
Details 0.1M MgCl2, 0.1M Sodium Acetate, 22% PEG400, 3%(v/v) dimethyl sulfoxide, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.32 α = 90
b = 163.05 β = 90
c = 39.57 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2011-08-05
Diffraction Radiation
Monochromator Protocol
Bartels Monochromator Crystal Type Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 0.97920 SLS X06DA

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
2.42 46.89 99.8 0.067 -- -- 7.77 27467 27467 -3.0 -3.0 46.5
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)
2.42 2.56 98.8 0.768 -- 2.43 7.54 4363

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 2.416 46.891 -- 1.99 27467 27362 1358 99.58 0.2371 0.2371 0.2353 0.271 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 2.4161 2.5025 -- 133 2588 0.3641 0.39 -- 98.0
X Ray Diffraction 2.5025 2.6027 -- 135 2605 0.3179 0.3614 -- 100.0
X Ray Diffraction 2.6027 2.7211 -- 136 2583 0.2906 0.2738 -- 100.0
X Ray Diffraction 2.7211 2.8646 -- 138 2638 0.2618 0.3229 -- 100.0
X Ray Diffraction 2.8646 3.044 -- 136 2619 0.2704 0.3344 -- 100.0
X Ray Diffraction 3.044 3.279 -- 134 2556 0.2418 0.2598 -- 99.0
X Ray Diffraction 3.279 3.6088 -- 140 2594 0.2439 0.2875 -- 100.0
X Ray Diffraction 3.6088 4.1308 -- 137 2597 0.2245 0.2658 -- 100.0
X Ray Diffraction 4.1308 5.2033 -- 131 2613 0.2086 0.246 -- 100.0
X Ray Diffraction 5.2033 46.8995 -- 138 2611 0.1921 0.224 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 68.9097
Anisotropic B[1][1] 14.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -7.5335
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.4665
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 27.192
f_plane_restr 0.003
f_chiral_restr 0.046
f_angle_d 0.979
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 931
Nucleic Acid Atoms 1060
Heterogen Atoms 0
Solvent Atoms 62

Software

Computing
Computing Package Purpose
RemDAq Data Collection
XDS package Data Reduction (intensity integration)
XDS package Data Reduction (data scaling)
SHELXD, SHELXE Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
SHELXE model building
SHELXD model building
RemDAq data collection