X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Evaporation
pH 8
Temperature 293.0
Details 50 mM Tris-HCl pH 8.0, 50 mM sodium chloride, 5 mM magnesium chloride, 1 mM dithiothreitol, 50% glycerol, EVAPORATION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.88 α = 90
b = 100.25 β = 90
c = 136.7 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR DECTRIS PILATUS 6M -- 2013-04-15
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.97920 APS 24-ID-E

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
2.29 50 99.9 -- -- -- -- -- 43638 3.0 3.0 --
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)
2.294 2.38 99.6 -- -- -- -- --

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 2.294 48.863 -- 1.36 43638 43565 2000 99.53 -- 0.1774 0.175 0.2282 --
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 2.294 2.3512 -- 134 2778 0.2117 0.2795 -- 94.0
X Ray Diffraction 2.3512 2.4147 -- 142 2937 0.1919 0.2678 -- 100.0
X Ray Diffraction 2.4147 2.4858 -- 141 2929 0.1989 0.2578 -- 100.0
X Ray Diffraction 2.4858 2.566 -- 141 2947 0.1888 0.2709 -- 100.0
X Ray Diffraction 2.566 2.6577 -- 142 2949 0.188 0.2545 -- 100.0
X Ray Diffraction 2.6577 2.7641 -- 140 2928 0.1949 0.2575 -- 100.0
X Ray Diffraction 2.7641 2.8899 -- 143 2958 0.1939 0.264 -- 100.0
X Ray Diffraction 2.8899 3.0422 -- 143 2984 0.2009 0.3065 -- 100.0
X Ray Diffraction 3.0422 3.2328 -- 143 2952 0.1902 0.2642 -- 100.0
X Ray Diffraction 3.2328 3.4824 -- 143 2988 0.1883 0.2258 -- 100.0
X Ray Diffraction 3.4824 3.8327 -- 144 2994 0.1661 0.2361 -- 100.0
X Ray Diffraction 3.8327 4.387 -- 145 3005 0.1449 0.195 -- 100.0
X Ray Diffraction 4.387 5.5259 -- 146 3039 0.1473 0.1863 -- 100.0
X Ray Diffraction 5.5259 48.8736 -- 153 3177 0.1841 0.1999 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.078
f_dihedral_angle_d 15.565
f_angle_d 1.165
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6473
Nucleic Acid Atoms 222
Heterogen Atoms 0
Solvent Atoms 288

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phaser-MR Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.2_1309) refinement
Phaser-MR model building
HKL-2000 data collection