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 = 116.91 α = 90
b = 116.91 β = 90
c = 183.76 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
3.3 50 98.0 0.08 0.08 -- 5.7 -- 41533 -3.0 0.0 116.06
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)
3.3 3.42 100.0 0.461 0.461 3.512 5.7 4232

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 3.3 29.403 -- 1.96 -- 41250 4164 97.77 -- 0.1805 0.1762 0.2181 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 3.3 3.3375 -- 146 1268 0.2966 0.3576 -- 100.0
X Ray Diffraction 3.3375 3.3767 -- 108 1248 0.2589 0.3095 -- 100.0
X Ray Diffraction 3.3767 3.4178 -- 135 1313 0.2633 0.3319 -- 99.0
X Ray Diffraction 3.4178 3.461 -- 127 1248 0.2608 0.3515 -- 99.0
X Ray Diffraction 3.461 3.5065 -- 135 1286 0.2354 0.3219 -- 99.0
X Ray Diffraction 3.5065 3.5545 -- 142 1241 0.2194 0.2726 -- 99.0
X Ray Diffraction 3.5545 3.6051 -- 142 1238 0.2206 0.2348 -- 100.0
X Ray Diffraction 3.6051 3.6589 -- 124 1284 0.2126 0.2735 -- 99.0
X Ray Diffraction 3.6589 3.7159 -- 138 1247 0.1984 0.2384 -- 99.0
X Ray Diffraction 3.7159 3.7767 -- 160 1265 0.1754 0.2302 -- 100.0
X Ray Diffraction 3.7767 3.8417 -- 148 1225 0.1803 0.2377 -- 100.0
X Ray Diffraction 3.8417 3.9114 -- 161 1289 0.1647 0.2005 -- 99.0
X Ray Diffraction 3.9114 3.9865 -- 114 1216 0.1612 0.1994 -- 99.0
X Ray Diffraction 3.9865 4.0676 -- 143 1263 0.1614 0.233 -- 99.0
X Ray Diffraction 4.0676 4.1558 -- 147 1275 0.1553 0.2202 -- 100.0
X Ray Diffraction 4.1558 4.2522 -- 158 1244 0.1571 0.209 -- 100.0
X Ray Diffraction 4.2522 4.3583 -- 154 1261 0.1329 0.1937 -- 100.0
X Ray Diffraction 4.3583 4.4757 -- 139 1262 0.122 0.1741 -- 100.0
X Ray Diffraction 4.4757 4.6069 -- 166 1226 0.117 0.1503 -- 100.0
X Ray Diffraction 4.6069 4.755 -- 140 1266 0.1197 0.1706 -- 100.0
X Ray Diffraction 4.755 4.9242 -- 142 1263 0.1239 0.1648 -- 100.0
X Ray Diffraction 4.9242 5.1204 -- 135 1275 0.1407 0.1797 -- 100.0
X Ray Diffraction 5.1204 5.3521 -- 140 1282 0.1437 0.2172 -- 100.0
X Ray Diffraction 5.3521 5.6324 -- 144 1242 0.1563 0.2234 -- 100.0
X Ray Diffraction 5.6324 5.9825 -- 158 1248 0.173 0.209 -- 100.0
X Ray Diffraction 5.9825 6.44 -- 135 1299 0.176 0.2271 -- 100.0
X Ray Diffraction 6.44 7.0798 -- 134 1251 0.1713 0.2336 -- 100.0
X Ray Diffraction 7.0798 8.0856 -- 141 1271 0.1702 0.2027 -- 100.0
X Ray Diffraction 8.0856 10.1176 -- 135 1153 0.1678 0.1685 -- 92.0
X Ray Diffraction 10.1176 29.4043 -- 73 637 0.2486 0.2285 -- 50.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic+TLS
Mean Isotropic B 136.591
Anisotropic B[1][1] 1.332
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.332
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -49.123
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.231
f_plane_restr 0.006
f_chiral_restr 0.082
f_angle_d 1.295
f_bond_d 0.027
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10079
Nucleic Acid Atoms 730
Heterogen Atoms 2
Solvent Atoms 7

Software

Computing
Computing Package Purpose
GDA Data Collection
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
GDA data collection