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 253 with the SMILES code C[C@@H](CN)N1C[C@H](C)O[C@H](C)C1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.33 α = 90
b = 72.94 β = 109.48
c = 52.82 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 -- 2014-08-05
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
1.14 42.74 99.5 0.041 -- -- 3.692 -- 117466 -- -3.0 10.47
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)
1.14 1.21 98.5 0.497 -- 2.38 -- --

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 1.139 28.125 -- 1.36 -- 117460 5873 99.56 -- 0.1314 0.1307 0.1448 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 1.1392 1.1521 -- 185 3501 0.209 0.2282 -- 94.0
X Ray Diffraction 1.1521 1.1657 -- 195 3721 0.1979 0.2035 -- 100.0
X Ray Diffraction 1.1657 1.1799 -- 195 3707 0.1869 0.1926 -- 100.0
X Ray Diffraction 1.1799 1.1949 -- 196 3720 0.1797 0.1884 -- 100.0
X Ray Diffraction 1.1949 1.2106 -- 193 3668 0.1826 0.1984 -- 99.0
X Ray Diffraction 1.2106 1.2272 -- 197 3729 0.1735 0.2265 -- 99.0
X Ray Diffraction 1.2272 1.2447 -- 194 3690 0.1693 0.1843 -- 100.0
X Ray Diffraction 1.2447 1.2633 -- 197 3754 0.1588 0.1872 -- 100.0
X Ray Diffraction 1.2633 1.283 -- 195 3703 0.1524 0.1804 -- 100.0
X Ray Diffraction 1.283 1.304 -- 197 3728 0.1466 0.2024 -- 100.0
X Ray Diffraction 1.304 1.3265 -- 195 3705 0.1378 0.1761 -- 100.0
X Ray Diffraction 1.3265 1.3506 -- 195 3705 0.1361 0.1655 -- 100.0
X Ray Diffraction 1.3506 1.3766 -- 196 3736 0.1269 0.1439 -- 100.0
X Ray Diffraction 1.3766 1.4047 -- 196 3725 0.1152 0.1207 -- 100.0
X Ray Diffraction 1.4047 1.4353 -- 195 3701 0.1109 0.1319 -- 100.0
X Ray Diffraction 1.4353 1.4687 -- 197 3739 0.1039 0.1319 -- 100.0
X Ray Diffraction 1.4687 1.5054 -- 197 3739 0.1037 0.1306 -- 100.0
X Ray Diffraction 1.5054 1.5461 -- 195 3709 0.0963 0.1166 -- 100.0
X Ray Diffraction 1.5461 1.5916 -- 196 3734 0.0927 0.1136 -- 100.0
X Ray Diffraction 1.5916 1.6429 -- 196 3722 0.0933 0.1103 -- 100.0
X Ray Diffraction 1.6429 1.7016 -- 196 3725 0.0964 0.1102 -- 100.0
X Ray Diffraction 1.7016 1.7698 -- 197 3739 0.1005 0.1362 -- 100.0
X Ray Diffraction 1.7698 1.8503 -- 196 3726 0.1019 0.1155 -- 100.0
X Ray Diffraction 1.8503 1.9478 -- 195 3708 0.1075 0.1208 -- 100.0
X Ray Diffraction 1.9478 2.0698 -- 197 3728 0.1067 0.1241 -- 100.0
X Ray Diffraction 2.0698 2.2296 -- 196 3730 0.1128 0.1217 -- 100.0
X Ray Diffraction 2.2296 2.4538 -- 199 3775 0.1235 0.1314 -- 100.0
X Ray Diffraction 2.4538 2.8086 -- 197 3761 0.1352 0.136 -- 100.0
X Ray Diffraction 2.8086 3.5375 -- 198 3755 0.1469 0.1651 -- 100.0
X Ray Diffraction 3.5375 28.1334 -- 200 3804 0.1568 0.1569 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.7393
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 10.261
f_chiral_restr 0.07
f_plane_restr 0.006
f_angle_d 1.201
f_bond_d 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 265

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