X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details 4-5% isopropanol, optimised mixture of salts, 50mM Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 122.51 α = 90
b = 122.51 β = 90
c = 178.3 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-08-07
Diffraction Radiation
Monochromator Protocol
Double Crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 DIAMOND I03

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
3.1 50 99.2 0.075 0.075 -- 5.8 54325 53890 0.0 -3.0 98.815
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)
3.1 3.21 100.0 0.408 0.408 3.563 5.8 5435

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 3.1 34.127 -- 1.97 -- 53839 5392 99.15 -- 0.1902 0.186 0.2277 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 3.1001 3.1353 -- 180 1665 0.2805 0.3314 -- 100.0
X Ray Diffraction 3.1353 3.1722 -- 159 1597 0.2635 0.2883 -- 99.0
X Ray Diffraction 3.1722 3.2108 -- 168 1666 0.2676 0.3428 -- 100.0
X Ray Diffraction 3.2108 3.2515 -- 180 1583 0.2479 0.3407 -- 100.0
X Ray Diffraction 3.2515 3.2942 -- 194 1666 0.2192 0.2302 -- 100.0
X Ray Diffraction 3.2942 3.3393 -- 164 1633 0.2106 0.2714 -- 100.0
X Ray Diffraction 3.3393 3.387 -- 169 1642 0.2157 0.2693 -- 100.0
X Ray Diffraction 3.387 3.4375 -- 185 1610 0.216 0.2834 -- 100.0
X Ray Diffraction 3.4375 3.4911 -- 176 1685 0.2135 0.2533 -- 100.0
X Ray Diffraction 3.4911 3.5483 -- 169 1607 0.205 0.2674 -- 100.0
X Ray Diffraction 3.5483 3.6094 -- 170 1652 0.2228 0.2725 -- 100.0
X Ray Diffraction 3.6094 3.675 -- 170 1605 0.2267 0.3219 -- 100.0
X Ray Diffraction 3.675 3.7456 -- 169 1639 0.1959 0.2312 -- 100.0
X Ray Diffraction 3.7456 3.8219 -- 203 1608 0.1793 0.2299 -- 100.0
X Ray Diffraction 3.8219 3.9049 -- 194 1620 0.1595 0.2283 -- 100.0
X Ray Diffraction 3.9049 3.9956 -- 190 1599 0.1505 0.1836 -- 100.0
X Ray Diffraction 3.9956 4.0954 -- 182 1654 0.1656 0.2092 -- 100.0
X Ray Diffraction 4.0954 4.2059 -- 189 1634 0.1672 0.2091 -- 100.0
X Ray Diffraction 4.2059 4.3295 -- 194 1620 0.1562 0.2004 -- 100.0
X Ray Diffraction 4.3295 4.4689 -- 175 1597 0.1378 0.1814 -- 100.0
X Ray Diffraction 4.4689 4.6283 -- 195 1603 0.1236 0.151 -- 100.0
X Ray Diffraction 4.6283 4.8131 -- 211 1632 0.133 0.1791 -- 100.0
X Ray Diffraction 4.8131 5.0315 -- 181 1612 0.1494 0.1967 -- 100.0
X Ray Diffraction 5.0315 5.2958 -- 177 1641 0.1683 0.2083 -- 100.0
X Ray Diffraction 5.2958 5.6263 -- 180 1616 0.1767 0.2313 -- 100.0
X Ray Diffraction 5.6263 6.0585 -- 189 1633 0.1882 0.2172 -- 100.0
X Ray Diffraction 6.0585 6.6641 -- 182 1588 0.1831 0.2017 -- 100.0
X Ray Diffraction 6.6641 7.619 -- 164 1652 0.1836 0.2198 -- 100.0
X Ray Diffraction 7.619 9.564 -- 200 1614 0.1729 0.1954 -- 100.0
X Ray Diffraction 9.564 34.1288 -- 133 1274 0.2166 0.2603 -- 78.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic+TLS
Mean Isotropic B 112.623
Anisotropic B[1][1] -13.7173
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -13.7173
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.8126
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_chiral_restr 0.083
f_dihedral_angle_d 20.094
f_angle_d 1.308
f_bond_d 0.025
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10282
Nucleic Acid Atoms 730
Heterogen Atoms 54
Solvent Atoms 5

Software

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