X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 290.0
Details 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000; crystal obtained by streak-seeding and soaked with 90 mM of fragment 210 with the SMILES code CC1=CC(O)=C2C3=C(C=NN3)C=CC2=N1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.24 α = 90
b = 73.21 β = 109.26
c = 52.56 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2013-04-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1

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
1.08 41.08 99.6 0.066 -- -- 3.689 -- 137896 -- -3.0 8.81
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)
1.08 1.14 99.0 0.499 -- 2.19 -- --

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 1.079 36.889 -- 1.99 -- 137886 6894 99.63 -- 0.1454 0.1446 0.1619 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 1.0793 1.0916 -- 222 4220 0.2211 0.2261 -- 96.0
X Ray Diffraction 1.0916 1.1044 -- 229 4350 0.2086 0.2444 -- 100.0
X Ray Diffraction 1.1044 1.1179 -- 230 4368 0.1902 0.2023 -- 100.0
X Ray Diffraction 1.1179 1.132 -- 227 4320 0.1806 0.1936 -- 100.0
X Ray Diffraction 1.132 1.1469 -- 229 4357 0.1671 0.1721 -- 100.0
X Ray Diffraction 1.1469 1.1627 -- 233 4413 0.1619 0.1731 -- 100.0
X Ray Diffraction 1.1627 1.1793 -- 227 4315 0.1538 0.1687 -- 100.0
X Ray Diffraction 1.1793 1.1969 -- 229 4351 0.1479 0.1629 -- 100.0
X Ray Diffraction 1.1969 1.2156 -- 230 4371 0.1464 0.1594 -- 100.0
X Ray Diffraction 1.2156 1.2355 -- 230 4375 0.1453 0.1488 -- 100.0
X Ray Diffraction 1.2355 1.2568 -- 230 4366 0.1438 0.1683 -- 100.0
X Ray Diffraction 1.2568 1.2797 -- 228 4333 0.1446 0.1544 -- 100.0
X Ray Diffraction 1.2797 1.3043 -- 230 4378 0.1407 0.1509 -- 100.0
X Ray Diffraction 1.3043 1.3309 -- 231 4385 0.1333 0.1523 -- 100.0
X Ray Diffraction 1.3309 1.3598 -- 229 4339 0.129 0.1518 -- 100.0
X Ray Diffraction 1.3598 1.3915 -- 230 4380 0.1276 0.1448 -- 100.0
X Ray Diffraction 1.3915 1.4263 -- 232 4411 0.1252 0.1625 -- 100.0
X Ray Diffraction 1.4263 1.4648 -- 229 4348 0.1231 0.1667 -- 100.0
X Ray Diffraction 1.4648 1.5079 -- 231 4384 0.1239 0.146 -- 100.0
X Ray Diffraction 1.5079 1.5566 -- 229 4349 0.1206 0.1527 -- 100.0
X Ray Diffraction 1.5566 1.6123 -- 230 4368 0.1175 0.1396 -- 100.0
X Ray Diffraction 1.6123 1.6768 -- 230 4369 0.118 0.1461 -- 100.0
X Ray Diffraction 1.6768 1.7531 -- 231 4392 0.1235 0.1605 -- 100.0
X Ray Diffraction 1.7531 1.8455 -- 229 4361 0.1228 0.1432 -- 100.0
X Ray Diffraction 1.8455 1.9612 -- 233 4415 0.125 0.1262 -- 100.0
X Ray Diffraction 1.9612 2.1126 -- 228 4345 0.1226 0.1325 -- 100.0
X Ray Diffraction 2.1126 2.3251 -- 231 4382 0.1287 0.1417 -- 100.0
X Ray Diffraction 2.3251 2.6615 -- 232 4400 0.1469 0.1581 -- 100.0
X Ray Diffraction 2.6615 3.3529 -- 231 4401 0.1532 0.1693 -- 100.0
X Ray Diffraction 3.3529 36.9109 -- 234 4446 0.1795 0.1979 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.6759
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.071
f_plane_restr 0.006
f_angle_d 1.197
f_bond_d 0.006
f_dihedral_angle_d 10.723
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 216

Software

Software
Software Name Purpose
XDS data scaling
PHENIX refinement
PHASER phasing version: 2.5.7
PDB_EXTRACT data extraction version: 3.20
XDS data reduction