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_dihedral_angle_d 17.468
f_plane_restr 0.002
f_chiral_restr 0.036
f_angle_d 0.598
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction
DENZO data collection