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 16% PEG-400, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 176.32 α = 90
b = 39.83 β = 105.79
c = 73.49 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR PSI PILATUS 6M -- 2012-11-03
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 0.979590 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
2.78 48.25 98.1 -- 0.09 -- 6.68 23902 23902 -3.0 -3.0 65.815
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)
2.78 2.94 89.2 -- 0.761 2.31 5.76 3942

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 2.775 48.246 -- 2.0 23902 23806 1194 97.84 0.2426 0.2426 0.2415 0.2624 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 2.7755 2.8866 -- 114 2181 0.4199 0.4428 -- 85.0
X Ray Diffraction 2.8866 3.0179 -- 138 2545 0.3772 0.3904 -- 100.0
X Ray Diffraction 3.0179 3.177 -- 133 2545 0.3026 0.3715 -- 99.0
X Ray Diffraction 3.177 3.376 -- 134 2525 0.2558 0.2873 -- 98.0
X Ray Diffraction 3.376 3.6366 -- 133 2577 0.2555 0.278 -- 100.0
X Ray Diffraction 3.6366 4.0024 -- 136 2569 0.2173 0.2621 -- 100.0
X Ray Diffraction 4.0024 4.5812 -- 136 2529 0.1921 0.2017 -- 100.0
X Ray Diffraction 4.5812 5.7703 -- 135 2568 0.2071 0.2191 -- 100.0
X Ray Diffraction 5.7703 48.2536 -- 135 2573 0.2281 0.2337 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 100.071
Anisotropic B[1][1] 38.2239
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -9.5862
Anisotropic B[2][2] -20.5652
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -17.6587
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 26.205
f_angle_d 0.924
f_plane_restr 0.003
f_chiral_restr 0.043
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 912
Nucleic Acid Atoms 943
Heterogen Atoms 0
Solvent Atoms 41

Software

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