X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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 = 81.43 α = 90
b = 95.6 β = 90
c = 137.01 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
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 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 45.97 94.1 -- -- -- -- -- 220519 -- 1.34 --
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 61.1 -- -- 1.34 2.6 --

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 1.069 45.965 -- 1.34 -- 220519 11067 94.1 -- 0.1399 0.139 0.156 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 1.0687 1.0808 -- 211 3779 0.3171 0.3422 -- 51.0
X Ray Diffraction 1.0808 1.0935 -- 226 4499 0.2736 0.2949 -- 61.0
X Ray Diffraction 1.0935 1.1069 -- 303 5055 0.25 0.2655 -- 69.0
X Ray Diffraction 1.1069 1.1209 -- 301 5638 0.2187 0.254 -- 76.0
X Ray Diffraction 1.1209 1.1356 -- 311 6114 0.207 0.2319 -- 83.0
X Ray Diffraction 1.1356 1.1512 -- 367 6635 0.1842 0.2099 -- 90.0
X Ray Diffraction 1.1512 1.1676 -- 362 7021 0.1707 0.1809 -- 95.0
X Ray Diffraction 1.1676 1.1851 -- 365 7270 0.1524 0.1695 -- 99.0
X Ray Diffraction 1.1851 1.2036 -- 369 7358 0.1422 0.1733 -- 99.0
X Ray Diffraction 1.2036 1.2233 -- 371 7377 0.1361 0.1589 -- 99.0
X Ray Diffraction 1.2233 1.2444 -- 361 7355 0.1363 0.1532 -- 100.0
X Ray Diffraction 1.2444 1.2671 -- 389 7324 0.1286 0.1606 -- 100.0
X Ray Diffraction 1.2671 1.2914 -- 395 7404 0.1259 0.1543 -- 100.0
X Ray Diffraction 1.2914 1.3178 -- 391 7348 0.1241 0.1399 -- 100.0
X Ray Diffraction 1.3178 1.3464 -- 384 7413 0.1211 0.1434 -- 100.0
X Ray Diffraction 1.3464 1.3778 -- 374 7339 0.1181 0.1346 -- 100.0
X Ray Diffraction 1.3778 1.4122 -- 384 7421 0.1222 0.1338 -- 100.0
X Ray Diffraction 1.4122 1.4504 -- 378 7460 0.1177 0.1437 -- 100.0
X Ray Diffraction 1.4504 1.4931 -- 386 7371 0.1144 0.1504 -- 100.0
X Ray Diffraction 1.4931 1.5413 -- 383 7393 0.1102 0.1382 -- 100.0
X Ray Diffraction 1.5413 1.5964 -- 394 7437 0.1101 0.1242 -- 100.0
X Ray Diffraction 1.5964 1.6603 -- 404 7429 0.111 0.135 -- 100.0
X Ray Diffraction 1.6603 1.7359 -- 394 7391 0.1141 0.1399 -- 100.0
X Ray Diffraction 1.7359 1.8274 -- 382 7458 0.1212 0.1487 -- 100.0
X Ray Diffraction 1.8274 1.9419 -- 422 7421 0.1306 0.1412 -- 100.0
X Ray Diffraction 1.9419 2.0918 -- 384 7464 0.1322 0.1407 -- 100.0
X Ray Diffraction 2.0918 2.3023 -- 419 7456 0.134 0.1559 -- 100.0
X Ray Diffraction 2.3023 2.6354 -- 394 7522 0.1418 0.1484 -- 100.0
X Ray Diffraction 2.6354 3.3202 -- 426 7546 0.1492 0.1618 -- 100.0
X Ray Diffraction 3.3202 46.008 -- 437 7754 0.1491 0.1561 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 2.4982
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.0391
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.459
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.011
f_chiral_restr 0.1
f_dihedral_angle_d 13.237
f_angle_d 1.648
f_bond_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3940
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 575

Software

Computing
Computing Package Purpose
BluIce Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHENIX model building
BluIce data collection