X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.9
Temperature 298.0
Details 37-38% MPD, 0.1M Hepes/KOH, 20mM NaBr, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 165.1 α = 90
b = 77.74 β = 90
c = 104.81 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2008-12-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.97977 BESSY 14.1

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
1.8 50 97.6 0.096 -- -- 4.3 -- 122391 -- -3.0 23.685
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)
1.8 1.9 84.1 0.652 -- 2.36 -- --

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
FOURIER SYNTHESIS 1.8 48.725 -- 1.35 -- 122324 6030 97.56 -- 0.1556 0.1537 0.1915 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 1.8 1.8205 -- 115 2190 0.2558 0.269 -- 56.0
X Ray Diffraction 1.8205 1.8419 -- 150 2848 0.2428 0.2974 -- 73.0
X Ray Diffraction 1.8419 1.8643 -- 164 3999 0.2274 0.2464 -- 100.0
X Ray Diffraction 1.8643 1.8879 -- 190 3894 0.2138 0.2541 -- 100.0
X Ray Diffraction 1.8879 1.9128 -- 207 3933 0.2089 0.2528 -- 100.0
X Ray Diffraction 1.9128 1.939 -- 206 3961 0.1949 0.2228 -- 100.0
X Ray Diffraction 1.939 1.9667 -- 206 3919 0.1925 0.2036 -- 100.0
X Ray Diffraction 1.9667 1.9961 -- 204 3928 0.1923 0.2412 -- 100.0
X Ray Diffraction 1.9961 2.0272 -- 211 3910 0.1767 0.2209 -- 100.0
X Ray Diffraction 2.0272 2.0605 -- 209 3967 0.1697 0.2104 -- 100.0
X Ray Diffraction 2.0605 2.096 -- 202 3922 0.164 0.211 -- 100.0
X Ray Diffraction 2.096 2.1341 -- 208 3939 0.161 0.2133 -- 100.0
X Ray Diffraction 2.1341 2.1752 -- 206 3953 0.1602 0.1971 -- 100.0
X Ray Diffraction 2.1752 2.2196 -- 210 3938 0.157 0.2082 -- 100.0
X Ray Diffraction 2.2196 2.2678 -- 205 3916 0.1609 0.2264 -- 100.0
X Ray Diffraction 2.2678 2.3206 -- 208 3943 0.1543 0.2153 -- 100.0
X Ray Diffraction 2.3206 2.3786 -- 207 3976 0.1535 0.2258 -- 100.0
X Ray Diffraction 2.3786 2.4429 -- 208 3951 0.156 0.2122 -- 100.0
X Ray Diffraction 2.4429 2.5148 -- 208 3964 0.1507 0.2041 -- 100.0
X Ray Diffraction 2.5148 2.596 -- 204 3953 0.1418 0.1922 -- 100.0
X Ray Diffraction 2.596 2.6888 -- 215 3976 0.1454 0.1711 -- 100.0
X Ray Diffraction 2.6888 2.7964 -- 209 3953 0.1459 0.1942 -- 100.0
X Ray Diffraction 2.7964 2.9236 -- 205 3979 0.1407 0.1805 -- 100.0
X Ray Diffraction 2.9236 3.0778 -- 210 3982 0.1424 0.1718 -- 100.0
X Ray Diffraction 3.0778 3.2706 -- 209 4007 0.1356 0.1926 -- 100.0
X Ray Diffraction 3.2706 3.523 -- 212 4012 0.1282 0.1569 -- 100.0
X Ray Diffraction 3.523 3.8774 -- 208 4008 0.1222 0.1605 -- 100.0
X Ray Diffraction 3.8774 4.4382 -- 208 4048 0.1164 0.1434 -- 100.0
X Ray Diffraction 4.4382 5.5903 -- 212 4091 0.1419 0.1815 -- 100.0
X Ray Diffraction 5.5903 48.7427 -- 214 4234 0.1829 0.1711 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.5473
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.617
f_plane_restr 0.006
f_chiral_restr 0.092
f_angle_d 1.376
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9213
Nucleic Acid Atoms 0
Heterogen Atoms 200
Solvent Atoms 1389

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction