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_bond_d 0.002
f_angle_d 0.632
f_chiral_restr 0.04
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

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.8.1_1168
PDB_EXTRACT data extraction version: 3.11
Mar data collection
isomorphous phasing version: replacement