X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8.5
Temperature 289.0
Details 0.17 M sodium acetate, 0.085 M Tris, 25.5% PEG 4000, and 15% glycerol and directly frozen, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61 α = 90.02
b = 61.01 β = 89.98
c = 195.14 γ = 78.36
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NOIR-1 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 -- ALS 4.2.2

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
2.37 48.78 98.0 0.064 -- -- 1.99 -- 109647 -- 2.0 41.68
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)
2.37 2.45 96.6 0.302 -- 1.5 1.94 --

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 2.37 44.01 -- 1.96 -- 109273 5506 97.7 -- 0.205 0.204 0.241 --
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 2.37 2.3969 -- 186 3389 0.3201 0.3845 -- 96.0
X Ray Diffraction 2.3969 2.4251 -- 190 3366 0.2957 0.3322 -- 96.0
X Ray Diffraction 2.4251 2.4547 -- 190 3370 0.297 0.3487 -- 96.0
X Ray Diffraction 2.4547 2.4858 -- 189 3432 0.2927 0.3505 -- 96.0
X Ray Diffraction 2.4858 2.5185 -- 179 3402 0.2866 0.3282 -- 96.0
X Ray Diffraction 2.5185 2.553 -- 172 3536 0.3077 0.3721 -- 97.0
X Ray Diffraction 2.553 2.5894 -- 149 3367 0.2826 0.311 -- 97.0
X Ray Diffraction 2.5894 2.6281 -- 205 3409 0.2714 0.3533 -- 97.0
X Ray Diffraction 2.6281 2.6692 -- 183 3483 0.2635 0.3245 -- 97.0
X Ray Diffraction 2.6692 2.7129 -- 173 3428 0.2637 0.3006 -- 98.0
X Ray Diffraction 2.7129 2.7597 -- 194 3556 0.2562 0.284 -- 97.0
X Ray Diffraction 2.7597 2.8099 -- 183 3331 0.2484 0.3026 -- 98.0
X Ray Diffraction 2.8099 2.8639 -- 178 3478 0.2523 0.3032 -- 98.0
X Ray Diffraction 2.8639 2.9223 -- 183 3580 0.2518 0.3141 -- 98.0
X Ray Diffraction 2.9223 2.9859 -- 184 3333 0.2431 0.2835 -- 98.0
X Ray Diffraction 2.9859 3.0553 -- 206 3578 0.2371 0.2843 -- 98.0
X Ray Diffraction 3.0553 3.1317 -- 186 3387 0.25 0.303 -- 98.0
X Ray Diffraction 3.1317 3.2163 -- 184 3587 0.2352 0.2805 -- 99.0
X Ray Diffraction 3.2163 3.311 -- 192 3362 0.2169 0.2492 -- 98.0
X Ray Diffraction 3.311 3.4178 -- 171 3554 0.2032 0.2336 -- 99.0
X Ray Diffraction 3.4178 3.5399 -- 201 3453 0.1973 0.2187 -- 98.0
X Ray Diffraction 3.5399 3.6816 -- 190 3505 0.1885 0.2138 -- 98.0
X Ray Diffraction 3.6816 3.849 -- 193 3477 0.1862 0.224 -- 99.0
X Ray Diffraction 3.849 4.0518 -- 160 3539 0.1695 0.2067 -- 98.0
X Ray Diffraction 4.0518 4.3055 -- 182 3492 0.155 0.1802 -- 99.0
X Ray Diffraction 4.3055 4.6376 -- 186 3463 0.1459 0.1562 -- 99.0
X Ray Diffraction 4.6376 5.1036 -- 171 3550 0.1553 0.1892 -- 99.0
X Ray Diffraction 5.1036 5.8407 -- 170 3462 0.1733 0.2141 -- 99.0
X Ray Diffraction 5.8407 7.3531 -- 209 3482 0.185 0.2108 -- 99.0
X Ray Diffraction 7.3531 44.0195 -- 167 3416 0.1743 0.2021 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 47.46
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.048
f_dihedral_angle_d 15.495
f_angle_d 1.1
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14772
Nucleic Acid Atoms 2668
Heterogen Atoms 28
Solvent Atoms 729

Software

Computing
Computing Package Purpose
DTREK Data Reduction (intensity integration)
D*TREK Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (PHENIX.REFINE: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
D*trek data collection