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 = 54.61 α = 90
b = 79.46 β = 105.63
c = 54.96 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 2012-09-27
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
2.39 14 99.4 0.062 -- -- -- -- n/a -- -- 30.47
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)
2.4 2.49 95.3 0.26 -- -- -- 1695

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 2.394 13.737 -- 1.34 -- 33785 3358 96.85 -- 0.1822 0.1771 0.2276 --
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 2.3944 2.4285 -- 90 959 0.2309 0.2718 -- 72.0
X Ray Diffraction 2.4285 2.4645 -- 118 1132 0.2323 0.305 -- 85.0
X Ray Diffraction 2.4645 2.5028 -- 124 1187 0.232 0.3073 -- 91.0
X Ray Diffraction 2.5028 2.5436 -- 140 1239 0.23 0.3011 -- 93.0
X Ray Diffraction 2.5436 2.5871 -- 141 1240 0.2377 0.2792 -- 97.0
X Ray Diffraction 2.5871 2.6339 -- 152 1285 0.2153 0.3321 -- 98.0
X Ray Diffraction 2.6339 2.6842 -- 135 1289 0.2072 0.2443 -- 99.0
X Ray Diffraction 2.6842 2.7385 -- 173 1304 0.2114 0.2904 -- 99.0
X Ray Diffraction 2.7385 2.7976 -- 163 1222 0.1989 0.3134 -- 99.0
X Ray Diffraction 2.7976 2.8621 -- 129 1368 0.2083 0.293 -- 100.0
X Ray Diffraction 2.8621 2.933 -- 114 1294 0.1971 0.2621 -- 99.0
X Ray Diffraction 2.933 3.0115 -- 132 1347 0.2159 0.2981 -- 100.0
X Ray Diffraction 3.0115 3.0991 -- 135 1257 0.2126 0.2269 -- 99.0
X Ray Diffraction 3.0991 3.1979 -- 165 1314 0.1971 0.2867 -- 99.0
X Ray Diffraction 3.1979 3.3107 -- 158 1282 0.1838 0.2651 -- 100.0
X Ray Diffraction 3.3107 3.4413 -- 115 1346 0.173 0.2489 -- 99.0
X Ray Diffraction 3.4413 3.5952 -- 128 1269 0.1649 0.238 -- 100.0
X Ray Diffraction 3.5952 3.781 -- 147 1295 0.1595 0.2057 -- 99.0
X Ray Diffraction 3.781 4.0124 -- 165 1307 0.1498 0.1967 -- 99.0
X Ray Diffraction 4.0124 4.3132 -- 151 1273 0.1357 0.1735 -- 100.0
X Ray Diffraction 4.3132 4.7311 -- 128 1311 0.1361 0.1575 -- 99.0
X Ray Diffraction 4.7311 5.3794 -- 132 1344 0.1462 0.2001 -- 100.0
X Ray Diffraction 5.3794 6.6471 -- 141 1282 0.1624 0.1805 -- 100.0
X Ray Diffraction 6.6471 13.7369 -- 182 1281 0.1632 0.1648 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.3873
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.793
f_plane_restr 0.002
f_chiral_restr 0.04
f_angle_d 0.632
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2429
Nucleic Acid Atoms 627
Heterogen Atoms 16
Solvent Atoms 223

Software

Computing
Computing Package Purpose
Mar Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
isomorphous replacement Structure Solution
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