X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.9
Temperature 277.0
Details 5 mM DTT, 2 mM cellotetraose, 1 mM EDTA, 1.2 M K2HPO4, 0.8 M NaH2PO4

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.15 α = 90
b = 52.02 β = 90
c = 83.06 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 MX-300 Vertical Focusing Mirror: ultra-low expansion (ULE) titanium silicate flat mirror with Pt, Uncoated, and Pd strips 2014-10-09
Diffraction Radiation
Monochromator Protocol
ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1

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
0.97 44.09 96.2 0.065 -- -- 6.0 -- 111789 -- -3.0 7.29
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)
0.97 1.0 69.0 0.905 -- 1.26 -- --

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 0.97 44.087 -- 1.93 -- 212660 10613 95.0 -- 0.1231 0.1223 0.1367 --
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 0.97 0.981 -- 214 4115 0.387 0.4164 -- 57.0
X Ray Diffraction 0.981 0.9926 -- 239 4568 0.3504 0.3663 -- 65.0
X Ray Diffraction 0.9926 1.0047 -- 263 5239 0.3449 0.371 -- 74.0
X Ray Diffraction 1.0047 1.0174 -- 299 5690 0.3014 0.2806 -- 80.0
X Ray Diffraction 1.0174 1.0308 -- 320 6194 0.2665 0.2879 -- 87.0
X Ray Diffraction 1.0308 1.0449 -- 342 6589 0.2262 0.2366 -- 94.0
X Ray Diffraction 1.0449 1.0598 -- 365 7053 0.2071 0.2348 -- 99.0
X Ray Diffraction 1.0598 1.0757 -- 374 7122 0.184 0.1914 -- 100.0
X Ray Diffraction 1.0757 1.0925 -- 375 7036 0.1633 0.1709 -- 100.0
X Ray Diffraction 1.0925 1.1104 -- 376 7110 0.1543 0.1678 -- 100.0
X Ray Diffraction 1.1104 1.1295 -- 376 7070 0.1412 0.1393 -- 100.0
X Ray Diffraction 1.1295 1.1501 -- 368 7046 0.1225 0.1407 -- 100.0
X Ray Diffraction 1.1501 1.1722 -- 367 7058 0.1174 0.1439 -- 100.0
X Ray Diffraction 1.1722 1.1961 -- 371 7065 0.1122 0.13 -- 100.0
X Ray Diffraction 1.1961 1.2221 -- 377 7083 0.1106 0.1228 -- 100.0
X Ray Diffraction 1.2221 1.2506 -- 374 7064 0.1088 0.1267 -- 100.0
X Ray Diffraction 1.2506 1.2818 -- 371 7067 0.1046 0.127 -- 100.0
X Ray Diffraction 1.2818 1.3165 -- 368 7079 0.1002 0.1205 -- 100.0
X Ray Diffraction 1.3165 1.3552 -- 367 7046 0.0977 0.1207 -- 100.0
X Ray Diffraction 1.3552 1.399 -- 367 7115 0.0919 0.1257 -- 100.0
X Ray Diffraction 1.399 1.449 -- 379 7068 0.0891 0.107 -- 100.0
X Ray Diffraction 1.449 1.507 -- 373 7012 0.0878 0.1161 -- 99.0
X Ray Diffraction 1.507 1.5756 -- 376 7066 0.0843 0.097 -- 99.0
X Ray Diffraction 1.5756 1.6587 -- 372 7041 0.0796 0.0958 -- 99.0
X Ray Diffraction 1.6587 1.7626 -- 370 7025 0.0843 0.1105 -- 100.0
X Ray Diffraction 1.7626 1.8987 -- 376 7085 0.0899 0.1002 -- 100.0
X Ray Diffraction 1.8987 2.0897 -- 374 7086 0.0912 0.1072 -- 100.0
X Ray Diffraction 2.0897 2.3921 -- 376 7078 0.1034 0.1097 -- 100.0
X Ray Diffraction 2.3921 3.0137 -- 362 7097 0.1241 0.148 -- 100.0
X Ray Diffraction 3.0137 44.1328 -- 382 7080 0.1317 0.1329 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.9321
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.011
f_angle_d 1.624
f_plane_restr 0.009
f_dihedral_angle_d 12.652
f_chiral_restr 0.23
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1545
Nucleic Acid Atoms 0
Heterogen Atoms 110
Solvent Atoms 284

Software

Software
Software Name Purpose
XDS data scaling version: January 10, 2014
XSCALE data scaling version: January 10, 2014
PHASER phasing
PHENIX refinement version: 1.9-1692
PDB_EXTRACT data extraction version: 3.15