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 265 with the SMILES code CN1N=CC=C1\C=C1/CCOC2=C(C=CC=C2C)C1=O

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.28 α = 90
b = 73.13 β = 109.36
c = 52.65 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 -- 2013-07-18
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
1.07 41.09 98.6 0.033 -- -- 3.403 -- 140608 -- -3.0 9.92
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)
1.07 1.13 94.1 0.4 -- 2.55 -- --

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 1.069 39.505 -- 1.36 -- 140604 7030 98.67 -- 0.1251 0.1246 0.1353 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 1.0692 1.0814 -- 198 3760 0.2266 0.2251 -- 83.0
X Ray Diffraction 1.0814 1.0941 -- 229 4356 0.2017 0.2077 -- 97.0
X Ray Diffraction 1.0941 1.1075 -- 231 4390 0.1792 0.1939 -- 98.0
X Ray Diffraction 1.1075 1.1215 -- 229 4333 0.177 0.2028 -- 96.0
X Ray Diffraction 1.1215 1.1362 -- 231 4403 0.1489 0.1562 -- 98.0
X Ray Diffraction 1.1362 1.1518 -- 232 4403 0.1367 0.1552 -- 99.0
X Ray Diffraction 1.1518 1.1683 -- 233 4448 0.133 0.1476 -- 98.0
X Ray Diffraction 1.1683 1.1857 -- 234 4436 0.1272 0.1418 -- 99.0
X Ray Diffraction 1.1857 1.2042 -- 235 4465 0.1229 0.1374 -- 99.0
X Ray Diffraction 1.2042 1.224 -- 237 4506 0.1156 0.1289 -- 99.0
X Ray Diffraction 1.224 1.2451 -- 234 4447 0.1112 0.1248 -- 100.0
X Ray Diffraction 1.2451 1.2677 -- 235 4470 0.1083 0.1273 -- 100.0
X Ray Diffraction 1.2677 1.2921 -- 238 4517 0.1081 0.129 -- 100.0
X Ray Diffraction 1.2921 1.3185 -- 237 4502 0.1006 0.1198 -- 100.0
X Ray Diffraction 1.3185 1.3472 -- 235 4478 0.1016 0.1175 -- 100.0
X Ray Diffraction 1.3472 1.3785 -- 236 4483 0.1018 0.1248 -- 100.0
X Ray Diffraction 1.3785 1.413 -- 237 4500 0.0956 0.1112 -- 100.0
X Ray Diffraction 1.413 1.4512 -- 238 4520 0.0943 0.1255 -- 100.0
X Ray Diffraction 1.4512 1.4939 -- 236 4486 0.0924 0.0995 -- 100.0
X Ray Diffraction 1.4939 1.5421 -- 237 4499 0.0909 0.125 -- 100.0
X Ray Diffraction 1.5421 1.5972 -- 237 4506 0.0925 0.1091 -- 100.0
X Ray Diffraction 1.5972 1.6612 -- 237 4492 0.0975 0.118 -- 100.0
X Ray Diffraction 1.6612 1.7368 -- 237 4510 0.0988 0.1117 -- 100.0
X Ray Diffraction 1.7368 1.8283 -- 237 4500 0.1036 0.1152 -- 100.0
X Ray Diffraction 1.8283 1.9429 -- 237 4506 0.1073 0.1161 -- 100.0
X Ray Diffraction 1.9429 2.0929 -- 238 4528 0.1073 0.1285 -- 100.0
X Ray Diffraction 2.0929 2.3035 -- 236 4482 0.1118 0.1105 -- 100.0
X Ray Diffraction 2.3035 2.6367 -- 238 4520 0.1294 0.1288 -- 99.0
X Ray Diffraction 2.6367 3.3218 -- 240 4549 0.1415 0.1291 -- 100.0
X Ray Diffraction 3.3218 39.5321 -- 241 4579 0.1627 0.1771 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.4016
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.006
f_angle_d 1.202
f_chiral_restr 0.072
f_plane_restr 0.006
f_dihedral_angle_d 10.72
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 256

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