X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 292.0
Details 0.02M Tris pH7.5, 0.05M NaCl, 0.001M MnCl2, 0.002M MgCl2, 1mM TCEP, 0.15M MES pH6.5, 0.27M NaBr, 11.4-12.2% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 154.09 α = 90
b = 107.44 β = 110.63
c = 150.46 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 PSI PILATUS 6M -- 2011-10-28
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 0.9199 SLS X10SA

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
2.81 49.64 87.4 0.176 -- -- 12.8 99137 99137 0.0 -3.0 59.5
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)
2.8 3.0 56.5 0.548 -- 1.89 2.5 11922

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 2.805 49.638 -- 1.99 99137 99101 4956 87.86 0.1846 0.1846 0.1825 0.2239 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 2.8046 2.8365 1336 70 1336 0.3046 0.3492 -- 38.0
X Ray Diffraction 2.8365 2.8698 2015 106 2015 0.2932 0.3581 -- 57.0
X Ray Diffraction 2.8698 2.9048 2312 122 2312 0.2938 0.3046 -- 64.0
X Ray Diffraction 2.9048 2.9416 2233 117 2233 0.2924 0.3456 -- 64.0
X Ray Diffraction 2.9416 2.9803 2316 122 2316 0.2869 0.3634 -- 64.0
X Ray Diffraction 2.9803 3.0211 2217 117 2217 0.2787 0.3229 -- 63.0
X Ray Diffraction 3.0211 3.0643 2287 120 2287 0.2636 0.3362 -- 64.0
X Ray Diffraction 3.0643 3.11 2256 119 2256 0.2602 0.3132 -- 64.0
X Ray Diffraction 3.11 3.1586 2516 133 2516 0.2539 0.2924 -- 71.0
X Ray Diffraction 3.1586 3.2104 3109 163 3109 0.2524 0.3102 -- 87.0
X Ray Diffraction 3.2104 3.2657 3510 185 3510 0.2401 0.293 -- 99.0
X Ray Diffraction 3.2657 3.3251 3532 186 3532 0.233 0.309 -- 100.0
X Ray Diffraction 3.3251 3.389 3541 186 3541 0.219 0.2526 -- 100.0
X Ray Diffraction 3.389 3.4582 3589 189 3589 0.2142 0.2614 -- 100.0
X Ray Diffraction 3.4582 3.5334 3544 187 3544 0.1959 0.2645 -- 100.0
X Ray Diffraction 3.5334 3.6155 3574 188 3574 0.1948 0.2249 -- 100.0
X Ray Diffraction 3.6155 3.7059 3567 188 3567 0.1853 0.2292 -- 100.0
X Ray Diffraction 3.7059 3.8061 3539 186 3539 0.176 0.2475 -- 100.0
X Ray Diffraction 3.8061 3.918 3585 189 3585 0.17 0.2031 -- 100.0
X Ray Diffraction 3.918 4.0445 3557 187 3557 0.1698 0.1905 -- 100.0
X Ray Diffraction 4.0445 4.1889 3589 189 3589 0.1593 0.2161 -- 100.0
X Ray Diffraction 4.1889 4.3566 3570 187 3570 0.1505 0.1891 -- 100.0
X Ray Diffraction 4.3566 4.5547 3568 188 3568 0.1432 0.1786 -- 100.0
X Ray Diffraction 4.5547 4.7947 3576 188 3576 0.1365 0.1722 -- 100.0
X Ray Diffraction 4.7947 5.0948 3612 191 3612 0.1433 0.176 -- 100.0
X Ray Diffraction 5.0948 5.4877 3561 187 3561 0.1577 0.2146 -- 100.0
X Ray Diffraction 5.4877 6.0391 3600 190 3600 0.1712 0.2358 -- 100.0
X Ray Diffraction 6.0391 6.9109 3610 190 3610 0.1814 0.2234 -- 100.0
X Ray Diffraction 6.9109 8.6994 3623 190 3623 0.1584 0.1779 -- 100.0
X Ray Diffraction 8.6994 49.6458 3701 196 3701 0.159 0.175 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.035
f_dihedral_angle_d 9.903
f_angle_d 0.542
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 25991
Nucleic Acid Atoms 540
Heterogen Atoms 54
Solvent Atoms 244

Software

Computing
Computing Package Purpose
RemDAQ Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1168) refinement
PHASER model building
RemDAQ data collection