X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details 100 mM Tris pH 8.5, 22% v/v PEG 400, 150 mM CaCl2, 0.5% v/v MPD [2-METHYL-2,4-PENTANEDIOL], vapor diffusion, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.25 α = 90
b = 95.55 β = 90
c = 137.35 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2011-07-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.03 APS 23-ID-B

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
1.07 50 93.2 0.063 -- -- 7.6 -- 217292 -- -- --
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)
1.07 1.11 57.6 0.572 -- -- 2.9 13317

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 1.07 45.978 -- 1.34 -- 217223 10840 93.16 -- 0.1379 0.1373 0.1503 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 1.07 1.0825 -- 188 3534 0.2996 0.3239 -- 48.0
X Ray Diffraction 1.0825 1.0952 -- 220 4201 0.2648 0.2624 -- 57.0
X Ray Diffraction 1.0952 1.1086 -- 256 4805 0.2327 0.2448 -- 66.0
X Ray Diffraction 1.1086 1.1226 -- 283 5397 0.2144 0.2485 -- 73.0
X Ray Diffraction 1.1226 1.1374 -- 302 5877 0.1984 0.2133 -- 80.0
X Ray Diffraction 1.1374 1.1529 -- 319 6225 0.1781 0.2206 -- 85.0
X Ray Diffraction 1.1529 1.1694 -- 332 6613 0.1603 0.183 -- 90.0
X Ray Diffraction 1.1694 1.1869 -- 373 6916 0.147 0.1742 -- 94.0
X Ray Diffraction 1.1869 1.2054 -- 347 7355 0.138 0.1705 -- 99.0
X Ray Diffraction 1.2054 1.2252 -- 348 7368 0.1308 0.1753 -- 100.0
X Ray Diffraction 1.2252 1.2463 -- 396 7314 0.1294 0.1484 -- 100.0
X Ray Diffraction 1.2463 1.269 -- 385 7372 0.1266 0.1475 -- 100.0
X Ray Diffraction 1.269 1.2934 -- 365 7375 0.1236 0.1471 -- 100.0
X Ray Diffraction 1.2934 1.3198 -- 389 7324 0.1198 0.1413 -- 100.0
X Ray Diffraction 1.3198 1.3485 -- 379 7390 0.125 0.1401 -- 100.0
X Ray Diffraction 1.3485 1.3799 -- 358 7374 0.12 0.1491 -- 100.0
X Ray Diffraction 1.3799 1.4144 -- 382 7329 0.1187 0.1448 -- 100.0
X Ray Diffraction 1.4144 1.4526 -- 384 7445 0.12 0.1386 -- 100.0
X Ray Diffraction 1.4526 1.4954 -- 383 7345 0.1181 0.1442 -- 100.0
X Ray Diffraction 1.4954 1.5436 -- 399 7337 0.1154 0.1266 -- 100.0
X Ray Diffraction 1.5436 1.5988 -- 394 7373 0.1134 0.1371 -- 100.0
X Ray Diffraction 1.5988 1.6628 -- 402 7402 0.1147 0.1334 -- 100.0
X Ray Diffraction 1.6628 1.7385 -- 393 7352 0.1198 0.1399 -- 100.0
X Ray Diffraction 1.7385 1.8302 -- 384 7432 0.1207 0.1405 -- 100.0
X Ray Diffraction 1.8302 1.9448 -- 400 7417 0.131 0.1265 -- 100.0
X Ray Diffraction 1.9448 2.095 -- 407 7381 0.1303 0.1367 -- 100.0
X Ray Diffraction 2.095 2.3058 -- 401 7442 0.1336 0.145 -- 100.0
X Ray Diffraction 2.3058 2.6394 -- 424 7445 0.1371 0.1422 -- 100.0
X Ray Diffraction 2.6394 3.3253 -- 404 7538 0.1465 0.1554 -- 100.0
X Ray Diffraction 3.3253 45.978 -- 443 7705 0.1505 0.1525 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.628
Anisotropic B[1][1] 2.6708
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.4524
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.2184
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.489
f_plane_restr 0.01
f_chiral_restr 0.095
f_angle_d 1.602
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3944
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 609

Software

Computing
Computing Package Purpose
BLUICE Data Collection
HKL Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction