X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 282.0
Details Protein solution was at 20 mg/mL containing 50 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM bME. Mother liqueur contained 0.2 M Na citrate (pH 4.6), 20% PEG 3,350. 20% glycerol was used as the cryoprotectant, vapor diffusion, hanging drop, temperature 282K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.09 α = 101.47
b = 94.03 β = 96.74
c = 155.2 γ = 79.86
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2012-12-12
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 0.978590 APS 21-ID-D

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
2.8 30 97.3 0.143 0.143 -- -- 115292 112207 0.0 -3.0 36.789
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)
2.8 2.87 97.8 0.539 -- 2.33 -- --

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 2.8 19.86 -- 1.99 115249 112188 5609 97.61 0.226 0.1762 0.1733 0.2313 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 2.7999 2.8316 -- 189 3595 0.2433 0.2965 -- 98.0
X Ray Diffraction 2.8316 2.8649 -- 188 3555 0.2442 0.3113 -- 98.0
X Ray Diffraction 2.8649 2.8997 -- 186 3549 0.2381 0.3224 -- 98.0
X Ray Diffraction 2.8997 2.9363 -- 188 3575 0.2504 0.3342 -- 98.0
X Ray Diffraction 2.9363 2.9748 -- 187 3535 0.2525 0.3416 -- 98.0
X Ray Diffraction 2.9748 3.0154 -- 186 3537 0.2359 0.3175 -- 98.0
X Ray Diffraction 3.0154 3.0583 -- 190 3610 0.2318 0.2951 -- 98.0
X Ray Diffraction 3.0583 3.1038 -- 184 3511 0.2165 0.3041 -- 97.0
X Ray Diffraction 3.1038 3.1521 -- 188 3572 0.2157 0.283 -- 98.0
X Ray Diffraction 3.1521 3.2036 -- 187 3545 0.2093 0.274 -- 98.0
X Ray Diffraction 3.2036 3.2586 -- 186 3542 0.2024 0.2852 -- 98.0
X Ray Diffraction 3.2586 3.3176 -- 188 3568 0.1999 0.2788 -- 97.0
X Ray Diffraction 3.3176 3.3811 -- 187 3555 0.1884 0.2621 -- 98.0
X Ray Diffraction 3.3811 3.4498 -- 189 3582 0.1855 0.2656 -- 97.0
X Ray Diffraction 3.4498 3.5244 -- 184 3487 0.1855 0.2314 -- 98.0
X Ray Diffraction 3.5244 3.6059 -- 187 3564 0.1801 0.254 -- 97.0
X Ray Diffraction 3.6059 3.6955 -- 186 3541 0.1702 0.2146 -- 97.0
X Ray Diffraction 3.6955 3.7948 -- 187 3554 0.1603 0.2309 -- 98.0
X Ray Diffraction 3.7948 3.9056 -- 187 3552 0.1544 0.1968 -- 97.0
X Ray Diffraction 3.9056 4.0307 -- 186 3515 0.1453 0.1907 -- 97.0
X Ray Diffraction 4.0307 4.1734 -- 186 3536 0.1492 0.2299 -- 97.0
X Ray Diffraction 4.1734 4.3389 -- 187 3563 0.1426 0.1872 -- 97.0
X Ray Diffraction 4.3389 4.5341 -- 188 3579 0.1345 0.2031 -- 98.0
X Ray Diffraction 4.5341 4.77 -- 188 3556 0.1326 0.1834 -- 98.0
X Ray Diffraction 4.77 5.0642 -- 187 3558 0.129 0.1683 -- 98.0
X Ray Diffraction 5.0642 5.4478 -- 187 3546 0.1382 0.1995 -- 98.0
X Ray Diffraction 5.4478 5.9824 -- 187 3553 0.1632 0.2011 -- 97.0
X Ray Diffraction 5.9824 6.8172 -- 187 3556 0.1627 0.2276 -- 98.0
X Ray Diffraction 6.8172 8.4763 -- 188 3578 0.1512 0.1693 -- 98.0
X Ray Diffraction 8.4763 19.8607 -- 184 3510 0.15 0.18 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.6265
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.787
f_plane_restr 0.007
f_chiral_restr 0.074
f_angle_d 1.253
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 26575
Nucleic Acid Atoms 0
Heterogen Atoms 116
Solvent Atoms 481

Software

Computing
Computing Package Purpose
HKL-3000 Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1066) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction