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 317 with the SMILES code O=S1(=O)[C@@H]2CCC[C@H]1C(CC1=CC=CC=C1)=C2

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.3 α = 90
b = 73.03 β = 109.51
c = 52.81 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
CCD MAR CCD 165 mm -- 2014-01-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.3 0.895 BESSY 14.3

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
1.1 42.7 98.1 0.074 -- -- 4.185 -- 128920 -- -3.0 8.05
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)
1.1 1.17 95.2 0.658 -- 2.51 -- --

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 1.099 20.738 -- 1.36 -- 128903 6444 98.16 -- 0.1319 0.1311 0.1488 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 1.099 1.1115 -- 196 3735 0.255 0.2411 -- 91.0
X Ray Diffraction 1.1115 1.1246 -- 211 4003 0.2145 0.253 -- 96.0
X Ray Diffraction 1.1246 1.1383 -- 209 3980 0.1957 0.2044 -- 96.0
X Ray Diffraction 1.1383 1.1527 -- 210 3994 0.1862 0.1933 -- 97.0
X Ray Diffraction 1.1527 1.1679 -- 212 4017 0.1774 0.2015 -- 96.0
X Ray Diffraction 1.1679 1.1839 -- 211 4007 0.158 0.1907 -- 97.0
X Ray Diffraction 1.1839 1.2008 -- 212 4037 0.1557 0.1737 -- 97.0
X Ray Diffraction 1.2008 1.2187 -- 212 4021 0.152 0.1678 -- 97.0
X Ray Diffraction 1.2187 1.2377 -- 212 4034 0.153 0.1748 -- 97.0
X Ray Diffraction 1.2377 1.258 -- 215 4071 0.1454 0.1597 -- 98.0
X Ray Diffraction 1.258 1.2797 -- 212 4032 0.1445 0.1638 -- 98.0
X Ray Diffraction 1.2797 1.303 -- 216 4103 0.1467 0.1691 -- 98.0
X Ray Diffraction 1.303 1.328 -- 213 4057 0.1355 0.1558 -- 98.0
X Ray Diffraction 1.328 1.3551 -- 216 4090 0.1231 0.1657 -- 98.0
X Ray Diffraction 1.3551 1.3846 -- 215 4086 0.114 0.1455 -- 99.0
X Ray Diffraction 1.3846 1.4168 -- 214 4074 0.1118 0.13 -- 99.0
X Ray Diffraction 1.4168 1.4522 -- 217 4116 0.1035 0.1368 -- 99.0
X Ray Diffraction 1.4522 1.4915 -- 215 4091 0.1009 0.1177 -- 99.0
X Ray Diffraction 1.4915 1.5353 -- 216 4096 0.0977 0.1127 -- 99.0
X Ray Diffraction 1.5353 1.5849 -- 218 4151 0.099 0.125 -- 99.0
X Ray Diffraction 1.5849 1.6415 -- 217 4129 0.0992 0.1274 -- 99.0
X Ray Diffraction 1.6415 1.7072 -- 218 4129 0.1016 0.1142 -- 99.0
X Ray Diffraction 1.7072 1.7849 -- 218 4144 0.1029 0.1357 -- 99.0
X Ray Diffraction 1.7849 1.8789 -- 219 4177 0.1056 0.1271 -- 100.0
X Ray Diffraction 1.8789 1.9965 -- 218 4143 0.106 0.1293 -- 100.0
X Ray Diffraction 1.9965 2.1505 -- 219 4160 0.1092 0.1161 -- 100.0
X Ray Diffraction 2.1505 2.3667 -- 219 4178 0.1152 0.1204 -- 100.0
X Ray Diffraction 2.3667 2.7085 -- 220 4176 0.1323 0.1499 -- 100.0
X Ray Diffraction 2.7085 3.41 -- 220 4183 0.1443 0.1564 -- 100.0
X Ray Diffraction 3.41 20.7413 -- 224 4245 0.1564 0.1715 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.8249
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.071
f_bond_d 0.006
f_angle_d 1.193
f_dihedral_angle_d 10.673
f_plane_restr 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 280

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