X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 291.0
Details 14% PEG 3350, 300 mM sodium acetate pH 9, 50 mM HEPES pH 7.5, vapor diffusion, hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.52 α = 90
b = 79.21 β = 106.24
c = 54.69 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 104
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate mirrors 2013-01-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
2.28 14 97.5 0.053 -- -- 3.3 -- n/a -- -- 33.48
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)
2.275 2.36 81.9 0.245 -- -- 2.3 1657

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
Isomorphous replacement 2.275 13.923 -- 1.34 -- 36691 3646 91.35 -- 0.1951 0.1915 0.2267 --
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 2.2751 2.3049 -- 92 740 0.25 0.3147 -- 54.0
X Ray Diffraction 2.3049 2.3363 -- 109 939 0.2485 0.2956 -- 67.0
X Ray Diffraction 2.3363 2.3695 -- 126 1017 0.2442 0.3329 -- 74.0
X Ray Diffraction 2.3695 2.4047 -- 82 1122 0.2436 0.2921 -- 79.0
X Ray Diffraction 2.4047 2.4421 -- 130 1166 0.2287 0.2904 -- 85.0
X Ray Diffraction 2.4421 2.4819 -- 131 1283 0.2348 0.2857 -- 90.0
X Ray Diffraction 2.4819 2.5245 -- 140 1291 0.234 0.3313 -- 92.0
X Ray Diffraction 2.5245 2.5701 -- 143 1310 0.2408 0.2959 -- 94.0
X Ray Diffraction 2.5701 2.6192 -- 150 1307 0.2218 0.3038 -- 94.0
X Ray Diffraction 2.6192 2.6723 -- 149 1296 0.2235 0.2922 -- 95.0
X Ray Diffraction 2.6723 2.73 -- 160 1346 0.2313 0.2696 -- 95.0
X Ray Diffraction 2.73 2.793 -- 175 1264 0.2145 0.3046 -- 96.0
X Ray Diffraction 2.793 2.8623 -- 130 1381 0.2197 0.2266 -- 96.0
X Ray Diffraction 2.8623 2.9389 -- 121 1369 0.2138 0.2609 -- 95.0
X Ray Diffraction 2.9389 3.0246 -- 146 1358 0.2209 0.263 -- 97.0
X Ray Diffraction 3.0246 3.1211 -- 137 1319 0.2116 0.2639 -- 96.0
X Ray Diffraction 3.1211 3.2313 -- 167 1320 0.1986 0.2614 -- 96.0
X Ray Diffraction 3.2313 3.359 -- 165 1339 0.1937 0.2626 -- 97.0
X Ray Diffraction 3.359 3.5095 -- 109 1369 0.1887 0.2007 -- 97.0
X Ray Diffraction 3.5095 3.6913 -- 157 1366 0.1701 0.2278 -- 97.0
X Ray Diffraction 3.6913 3.9177 -- 167 1345 0.1726 0.2128 -- 97.0
X Ray Diffraction 3.9177 4.2124 -- 151 1370 0.159 0.1576 -- 98.0
X Ray Diffraction 4.2124 4.6222 -- 132 1348 0.1486 0.1757 -- 98.0
X Ray Diffraction 4.6222 5.2592 -- 145 1341 0.1541 0.1711 -- 98.0
X Ray Diffraction 5.2592 6.5113 -- 148 1396 0.1849 0.185 -- 98.0
X Ray Diffraction 6.5113 13.923 -- 184 1343 0.1792 0.1817 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.6408
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.598
f_chiral_restr 0.036
f_dihedral_angle_d 17.468
f_plane_restr 0.002
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2316
Nucleic Acid Atoms 627
Heterogen Atoms 33
Solvent Atoms 234

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.8.1_1168
PDB_EXTRACT data extraction version: 3.11