X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 289.0
Details sitting drop, temperature 289K, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.64 α = 89.98
b = 60.63 β = 89.92
c = 194.68 γ = 78.68
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NOIR-1 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 -- ALS 4.2.2

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
2.17 45.6 97.8 0.055 -- -- 1.95 -- 140661 -- 2.0 --
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)
2.17 2.25 97.1 0.474 -- 1.5 1.94 --

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 2.17 45.58 -- 1.96 -- 140232 7082 97.5 -- 0.206 0.204 0.244 --
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 2.17 2.1947 -- 257 4341 0.3206 0.3866 -- 97.0
X Ray Diffraction 2.1947 2.2205 -- 231 4433 0.3184 0.3987 -- 97.0
X Ray Diffraction 2.2205 2.2476 -- 214 4515 0.309 0.3858 -- 96.0
X Ray Diffraction 2.2476 2.276 -- 227 4289 0.3081 0.3659 -- 96.0
X Ray Diffraction 2.276 2.306 -- 227 4398 0.2867 0.3128 -- 97.0
X Ray Diffraction 2.306 2.3376 -- 248 4520 0.27 0.307 -- 97.0
X Ray Diffraction 2.3376 2.371 -- 244 4234 0.2703 0.3158 -- 97.0
X Ray Diffraction 2.371 2.4063 -- 259 4536 0.2553 0.3291 -- 97.0
X Ray Diffraction 2.4063 2.4439 -- 240 4354 0.2697 0.3282 -- 97.0
X Ray Diffraction 2.4439 2.484 -- 231 4451 0.2731 0.3617 -- 97.0
X Ray Diffraction 2.484 2.5268 -- 236 4507 0.2553 0.3089 -- 98.0
X Ray Diffraction 2.5268 2.5728 -- 207 4396 0.2471 0.2895 -- 98.0
X Ray Diffraction 2.5728 2.6223 -- 259 4427 0.2576 0.3017 -- 98.0
X Ray Diffraction 2.6223 2.6758 -- 235 4432 0.2467 0.301 -- 98.0
X Ray Diffraction 2.6758 2.7339 -- 231 4502 0.2362 0.2992 -- 98.0
X Ray Diffraction 2.7339 2.7975 -- 237 4409 0.2286 0.2602 -- 98.0
X Ray Diffraction 2.7975 2.8675 -- 238 4522 0.2268 0.3145 -- 98.0
X Ray Diffraction 2.8675 2.945 -- 229 4378 0.2383 0.2837 -- 98.0
X Ray Diffraction 2.945 3.0316 -- 263 4566 0.2297 0.2738 -- 98.0
X Ray Diffraction 3.0316 3.1295 -- 241 4352 0.2227 0.2958 -- 98.0
X Ray Diffraction 3.1295 3.2413 -- 226 4469 0.2153 0.2279 -- 98.0
X Ray Diffraction 3.2413 3.371 -- 229 4526 0.2008 0.2525 -- 98.0
X Ray Diffraction 3.371 3.5244 -- 254 4385 0.1838 0.2229 -- 98.0
X Ray Diffraction 3.5244 3.7101 -- 244 4428 0.1734 0.194 -- 98.0
X Ray Diffraction 3.7101 3.9425 -- 231 4475 0.1639 0.2233 -- 98.0
X Ray Diffraction 3.9425 4.2467 -- 226 4502 0.1626 0.1877 -- 98.0
X Ray Diffraction 4.2467 4.6736 -- 233 4519 0.1451 0.157 -- 98.0
X Ray Diffraction 4.6736 5.349 -- 217 4451 0.1731 0.2013 -- 99.0
X Ray Diffraction 5.349 6.7357 -- 251 4496 0.1958 0.2097 -- 98.0
X Ray Diffraction 6.7357 45.592 -- 217 4337 0.1784 0.2042 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.96
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.048
f_dihedral_angle_d 13.559
f_angle_d 1.102
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14756
Nucleic Acid Atoms 2877
Heterogen Atoms 4
Solvent Atoms 1266

Software

Computing
Computing Package Purpose
DTREK Data Reduction (intensity integration)
DTREK Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (PHENIX.REFINE: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
D*trek version: 9.9.9.4D data reduction
D*trek data collection