X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 291.0
Details 50mM Imidazole, 350mM Sodium Acetate, 18% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.32 α = 90
b = 79.18 β = 105.53
c = 54.86 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 92 Mirrors 2011-09-26
Diffraction Radiation
Monochromator Protocol
mirrors VarimaxHF SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178 -- --

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 28 98.9 0.047 -- -- 5.2 209537 209537 0.0 -3.0 28.5
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 1.86 90.8 0.229 -- 3.0 1.7 --

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
MOLECULAR REPLACEMENT 1.8 22.098 -- 0.0 39766 39766 4016 95.47 0.202 0.1903 0.1871 0.2196 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 1.7981 1.8193 -- 107 974 0.2572 0.3263 -- 74.0
X Ray Diffraction 1.8193 1.8415 -- 117 1028 0.2454 0.3267 -- 79.0
X Ray Diffraction 1.8415 1.8648 -- 120 1067 0.2323 0.295 -- 85.0
X Ray Diffraction 1.8648 1.8893 -- 135 1154 0.2277 0.289 -- 88.0
X Ray Diffraction 1.8893 1.9152 -- 122 1115 0.221 0.2178 -- 91.0
X Ray Diffraction 1.9152 1.9425 -- 142 1212 0.2175 0.293 -- 92.0
X Ray Diffraction 1.9425 1.9715 -- 140 1185 0.2208 0.305 -- 94.0
X Ray Diffraction 1.9715 2.0023 -- 140 1238 0.2007 0.2779 -- 95.0
X Ray Diffraction 2.0023 2.0351 -- 142 1232 0.1935 0.2374 -- 97.0
X Ray Diffraction 2.0351 2.0701 -- 131 1266 0.1923 0.2494 -- 98.0
X Ray Diffraction 2.0701 2.1078 -- 143 1256 0.195 0.2339 -- 99.0
X Ray Diffraction 2.1078 2.1483 -- 142 1254 0.2039 0.2783 -- 98.0
X Ray Diffraction 2.1483 2.1921 -- 140 1282 0.2021 0.2553 -- 98.0
X Ray Diffraction 2.1921 2.2397 -- 138 1259 0.1957 0.2524 -- 98.0
X Ray Diffraction 2.2397 2.2917 -- 151 1267 0.1906 0.2361 -- 99.0
X Ray Diffraction 2.2917 2.349 -- 154 1261 0.1963 0.2369 -- 98.0
X Ray Diffraction 2.349 2.4124 -- 124 1266 0.1998 0.2348 -- 98.0
X Ray Diffraction 2.4124 2.4833 -- 123 1289 0.2006 0.273 -- 98.0
X Ray Diffraction 2.4833 2.5634 -- 145 1252 0.209 0.2479 -- 98.0
X Ray Diffraction 2.5634 2.6548 -- 146 1269 0.2016 0.2299 -- 98.0
X Ray Diffraction 2.6548 2.7609 -- 145 1262 0.2005 0.2493 -- 99.0
X Ray Diffraction 2.7609 2.8863 -- 146 1277 0.1915 0.23 -- 98.0
X Ray Diffraction 2.8863 3.0381 -- 163 1265 0.2021 0.2248 -- 99.0
X Ray Diffraction 3.0381 3.228 -- 155 1272 0.1917 0.2194 -- 100.0
X Ray Diffraction 3.228 3.4763 -- 144 1303 0.1746 0.1825 -- 100.0
X Ray Diffraction 3.4763 3.8245 -- 133 1305 0.1659 0.1871 -- 100.0
X Ray Diffraction 3.8245 4.3742 -- 139 1302 0.152 0.1774 -- 100.0
X Ray Diffraction 4.3742 5.497 -- 152 1300 0.1619 0.1676 -- 100.0
X Ray Diffraction 5.497 22.1 -- 137 1338 0.1839 0.1968 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Restrained
Mean Isotropic B 28.0
Anisotropic B[1][1] 2.641
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.2336
Anisotropic B[2][2] 0.738
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.379
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.057
f_dihedral_angle_d 19.131
f_angle_d 1.027
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2577
Nucleic Acid Atoms 632
Heterogen Atoms 33
Solvent Atoms 563

Software

Computing
Computing Package Purpose
StructureStudio Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
CNS model building
StructureStudio data collection