X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.75
Temperature 291.0
Details 23% PEG 4000, 0.1 M SODIUM ACETATE PH 4.75, 0.2 M AMMONIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.86 α = 90
b = 88.91 β = 90
c = 176.4 γ = 90
Symmetry
Space Group P 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2010-09-09
Diffraction Radiation
Monochromator Protocol
SI(311) AND SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.97627 ESRF ID29

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
1.85 50 96.4 0.052 -- -- -- 113930 109841 2.0 -3.0 37.411
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)
1.849 1.96 96.2 0.46 -- 2.07 -- --

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 1.849 49.046 -- 1.21 113930 109841 5471 96.41 -- 0.1739 0.1721 0.2087 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 1.849 1.8705 -- 167 3261 0.2743 0.3089 -- 89.0
X Ray Diffraction 1.8705 1.8925 -- 187 3574 0.2601 0.2897 -- 98.0
X Ray Diffraction 1.8925 1.9155 -- 182 3484 0.2633 0.2912 -- 98.0
X Ray Diffraction 1.9155 1.9398 -- 183 3518 0.2404 0.2835 -- 98.0
X Ray Diffraction 1.9398 1.9653 -- 181 3512 0.2318 0.2842 -- 98.0
X Ray Diffraction 1.9653 1.9922 -- 188 3603 0.2231 0.2528 -- 98.0
X Ray Diffraction 1.9922 2.0207 -- 189 3513 0.222 0.2693 -- 98.0
X Ray Diffraction 2.0207 2.0509 -- 187 3495 0.2047 0.2872 -- 98.0
X Ray Diffraction 2.0509 2.0829 -- 191 3623 0.2012 0.2525 -- 98.0
X Ray Diffraction 2.0829 2.1171 -- 187 3521 0.1926 0.2747 -- 98.0
X Ray Diffraction 2.1171 2.1536 -- 184 3544 0.1828 0.2102 -- 98.0
X Ray Diffraction 2.1536 2.1927 -- 188 3554 0.173 0.2068 -- 98.0
X Ray Diffraction 2.1927 2.2349 -- 179 3517 0.1628 0.2046 -- 98.0
X Ray Diffraction 2.2349 2.2805 -- 183 3511 0.1754 0.2281 -- 98.0
X Ray Diffraction 2.2805 2.3301 -- 183 3514 0.1726 0.2124 -- 98.0
X Ray Diffraction 2.3301 2.3843 -- 184 3499 0.1795 0.2034 -- 97.0
X Ray Diffraction 2.3843 2.4439 -- 186 3535 0.183 0.2293 -- 97.0
X Ray Diffraction 2.4439 2.51 -- 180 3445 0.1717 0.2162 -- 97.0
X Ray Diffraction 2.51 2.5839 -- 187 3571 0.1835 0.2485 -- 98.0
X Ray Diffraction 2.5839 2.6673 -- 185 3474 0.1797 0.2342 -- 97.0
X Ray Diffraction 2.6673 2.7626 -- 188 3517 0.18 0.2744 -- 97.0
X Ray Diffraction 2.7626 2.8732 -- 185 3444 0.1672 0.1883 -- 97.0
X Ray Diffraction 2.8732 3.0039 -- 179 3479 0.1673 0.1944 -- 96.0
X Ray Diffraction 3.0039 3.1623 -- 172 3381 0.1727 0.2174 -- 93.0
X Ray Diffraction 3.1623 3.3604 -- 183 3436 0.1732 0.218 -- 95.0
X Ray Diffraction 3.3604 3.6197 -- 177 3416 0.1712 0.2104 -- 95.0
X Ray Diffraction 3.6197 3.9839 -- 178 3403 0.1512 0.1745 -- 94.0
X Ray Diffraction 3.9839 4.56 -- 173 3303 0.1327 0.1785 -- 92.0
X Ray Diffraction 4.56 5.7437 -- 178 3345 0.1511 0.1753 -- 93.0
X Ray Diffraction 5.7437 49.0636 -- 177 3378 0.1608 0.1564 -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.1342
Anisotropic B[1][1] -2.7434
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.6697
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0737
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 21.073
f_plane_restr 0.005
f_chiral_restr 0.071
f_angle_d 1.369
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4541
Nucleic Acid Atoms 0
Heterogen Atoms 130
Solvent Atoms 438

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
DM density modification
Phaser molecular replacement
Xscale data reduction