X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Sitting Drop Vapor Diffuction
pH 7.5
Temperature 298.0
Details Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT, 5 mM MgCl); Reservoir (0.2 M Lithium Sulfate, 0.1 M Sodium Acetate, 0.1 M HEPES, 25% PEG4000); Cryoprotection (Reservoir, + 20% glycerol and 50 mM MgCl), sitting drop vapor diffuction, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.84 α = 90
b = 124.85 β = 90
c = 139.09 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE MIRRORS 2012-01-01
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID

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
1.7 139.09 99.7 0.112 0.112 -- 6.9 210738 210738 0.0 0.0 --
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)
1.7 1.79 99.1 0.531 0.531 1.4 6.4 30329

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 1.7 28.477 0.0 0.0 210083 210083 10561 99.4 0.1535 0.1535 0.1521 0.1791 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 1.7 1.7193 -- 343 6499 0.2127 0.2432 -- 99.0
X Ray Diffraction 1.7193 1.7395 -- 352 6578 0.208 0.2623 -- 99.0
X Ray Diffraction 1.7395 1.7607 -- 332 6568 0.1993 0.2466 -- 99.0
X Ray Diffraction 1.7607 1.783 -- 359 6554 0.1988 0.232 -- 99.0
X Ray Diffraction 1.783 1.8065 -- 348 6530 0.1886 0.2402 -- 99.0
X Ray Diffraction 1.8065 1.8312 -- 352 6564 0.1773 0.2126 -- 99.0
X Ray Diffraction 1.8312 1.8574 -- 365 6608 0.1759 0.2315 -- 99.0
X Ray Diffraction 1.8574 1.8851 -- 361 6534 0.1693 0.2055 -- 99.0
X Ray Diffraction 1.8851 1.9146 -- 339 6577 0.1701 0.2206 -- 99.0
X Ray Diffraction 1.9146 1.9459 -- 332 6637 0.1618 0.2034 -- 99.0
X Ray Diffraction 1.9459 1.9795 -- 359 6614 0.1615 0.2112 -- 99.0
X Ray Diffraction 1.9795 2.0155 -- 347 6635 0.1563 0.204 -- 100.0
X Ray Diffraction 2.0155 2.0542 -- 348 6610 0.1521 0.1994 -- 100.0
X Ray Diffraction 2.0542 2.0961 -- 330 6655 0.1552 0.1959 -- 100.0
X Ray Diffraction 2.0961 2.1417 -- 382 6612 0.1547 0.1796 -- 100.0
X Ray Diffraction 2.1417 2.1915 -- 357 6637 0.1543 0.1875 -- 100.0
X Ray Diffraction 2.1915 2.2463 -- 349 6610 0.153 0.1891 -- 100.0
X Ray Diffraction 2.2463 2.307 -- 362 6652 0.1498 0.1897 -- 100.0
X Ray Diffraction 2.307 2.3749 -- 356 6629 0.1489 0.1745 -- 100.0
X Ray Diffraction 2.3749 2.4515 -- 322 6685 0.1484 0.1808 -- 100.0
X Ray Diffraction 2.4515 2.539 -- 351 6673 0.156 0.1781 -- 100.0
X Ray Diffraction 2.539 2.6406 -- 341 6682 0.1545 0.1976 -- 100.0
X Ray Diffraction 2.6406 2.7607 -- 363 6663 0.1524 0.1929 -- 100.0
X Ray Diffraction 2.7607 2.9061 -- 338 6707 0.1566 0.1816 -- 100.0
X Ray Diffraction 2.9061 3.088 -- 374 6704 0.1566 0.1773 -- 100.0
X Ray Diffraction 3.088 3.3261 -- 352 6718 0.1421 0.1531 -- 100.0
X Ray Diffraction 3.3261 3.6602 -- 368 6755 0.139 0.163 -- 100.0
X Ray Diffraction 3.6602 4.1884 -- 382 6762 0.123 0.1332 -- 100.0
X Ray Diffraction 4.1884 5.2715 -- 343 6871 0.1289 0.1458 -- 100.0
X Ray Diffraction 5.2715 28.4809 -- 354 6999 0.1649 0.1685 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.9951
Anisotropic B[1][1] 9.727
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.7479
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.979
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_bond_d 0.011
f_chiral_restr 0.071
f_dihedral_angle_d 12.929
f_angle_d 1.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13696
Nucleic Acid Atoms 0
Heterogen Atoms 98
Solvent Atoms 1973

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.16
PHENIX refinement version: 1.7.3_928
PDB_EXTRACT data extraction version: 3.11
MOSFLM data reduction
PHENIX phasing