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 360 with the SMILES code CC1=NN(CC2=CSC(=C2)C(O)=O)C(C)=C1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.35 α = 90
b = 73.05 β = 109.6
c = 52.92 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 -- 2013-12-14
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 41.18 93.1 0.035 -- -- 3.858 -- 133203 -- -3.0 9.84
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 85.3 0.387 -- 3.18 -- --

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 1.07 41.179 -- 1.36 -- 133197 6661 93.23 -- 0.1257 0.1251 0.1364 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 1.0697 1.0819 -- 185 3507 0.189 0.1884 -- 78.0
X Ray Diffraction 1.0819 1.0946 -- 206 3909 0.1767 0.2109 -- 87.0
X Ray Diffraction 1.0946 1.108 -- 207 3937 0.1601 0.1613 -- 87.0
X Ray Diffraction 1.108 1.122 -- 208 3943 0.1479 0.1613 -- 89.0
X Ray Diffraction 1.122 1.1367 -- 211 4018 0.1334 0.1709 -- 88.0
X Ray Diffraction 1.1367 1.1523 -- 208 3958 0.1288 0.1479 -- 89.0
X Ray Diffraction 1.1523 1.1688 -- 211 4010 0.1227 0.1343 -- 88.0
X Ray Diffraction 1.1688 1.1862 -- 214 4064 0.1173 0.1333 -- 90.0
X Ray Diffraction 1.1862 1.2048 -- 215 4075 0.1142 0.1281 -- 90.0
X Ray Diffraction 1.2048 1.2245 -- 217 4116 0.1082 0.1377 -- 91.0
X Ray Diffraction 1.2245 1.2456 -- 217 4126 0.1076 0.1234 -- 92.0
X Ray Diffraction 1.2456 1.2683 -- 219 4169 0.1057 0.1313 -- 92.0
X Ray Diffraction 1.2683 1.2927 -- 225 4277 0.1062 0.1378 -- 94.0
X Ray Diffraction 1.2927 1.3191 -- 224 4246 0.1027 0.1143 -- 94.0
X Ray Diffraction 1.3191 1.3478 -- 224 4265 0.1037 0.137 -- 95.0
X Ray Diffraction 1.3478 1.3791 -- 225 4275 0.099 0.1172 -- 95.0
X Ray Diffraction 1.3791 1.4136 -- 226 4296 0.0946 0.1229 -- 95.0
X Ray Diffraction 1.4136 1.4518 -- 229 4341 0.094 0.1127 -- 96.0
X Ray Diffraction 1.4518 1.4945 -- 228 4331 0.0947 0.1015 -- 96.0
X Ray Diffraction 1.4945 1.5428 -- 227 4316 0.0914 0.1057 -- 96.0
X Ray Diffraction 1.5428 1.5979 -- 230 4366 0.0959 0.1201 -- 96.0
X Ray Diffraction 1.5979 1.6619 -- 230 4375 0.0997 0.1029 -- 97.0
X Ray Diffraction 1.6619 1.7375 -- 230 4379 0.1035 0.1138 -- 97.0
X Ray Diffraction 1.7375 1.8292 -- 232 4398 0.1081 0.11 -- 97.0
X Ray Diffraction 1.8292 1.9438 -- 233 4426 0.1106 0.1128 -- 98.0
X Ray Diffraction 1.9438 2.0938 -- 233 4422 0.1132 0.1233 -- 98.0
X Ray Diffraction 2.0938 2.3045 -- 235 4473 0.1158 0.1314 -- 98.0
X Ray Diffraction 2.3045 2.6379 -- 234 4455 0.1341 0.1274 -- 98.0
X Ray Diffraction 2.6379 3.3233 -- 238 4517 0.1457 0.1505 -- 99.0
X Ray Diffraction 3.3233 41.2091 -- 240 4546 0.163 0.1787 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.3048
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_angle_d 1.209
f_chiral_restr 0.071
f_bond_d 0.006
f_dihedral_angle_d 10.704
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 260

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