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 168 with the SMILES code OCCNC(=O)\C=C\C1=CC=CS1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.27 α = 90
b = 73.16 β = 109.63
c = 52.71 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 -- 2013-04-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.3 0.8944 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
1.26 42.64 99.2 0.069 -- -- 4.144 -- 87213 -- -3.0 8.95
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)
1.26 1.33 96.1 0.676 -- 2.28 -- --

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 1.257 34.81 -- 1.99 -- 87212 4361 99.3 -- 0.1315 0.1304 0.1542 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 1.2568 1.271 -- 117 2230 0.2213 0.2546 -- 81.0
X Ray Diffraction 1.271 1.286 -- 148 2810 0.204 0.2217 -- 100.0
X Ray Diffraction 1.286 1.3017 -- 143 2721 0.1884 0.2089 -- 100.0
X Ray Diffraction 1.3017 1.3182 -- 148 2803 0.1777 0.2134 -- 100.0
X Ray Diffraction 1.3182 1.3355 -- 144 2746 0.1722 0.2013 -- 100.0
X Ray Diffraction 1.3355 1.3538 -- 147 2785 0.1635 0.1971 -- 100.0
X Ray Diffraction 1.3538 1.3731 -- 145 2748 0.1579 0.189 -- 100.0
X Ray Diffraction 1.3731 1.3936 -- 146 2782 0.1489 0.1749 -- 100.0
X Ray Diffraction 1.3936 1.4154 -- 146 2779 0.1397 0.1731 -- 100.0
X Ray Diffraction 1.4154 1.4386 -- 145 2739 0.1336 0.1749 -- 100.0
X Ray Diffraction 1.4386 1.4634 -- 147 2802 0.123 0.1458 -- 100.0
X Ray Diffraction 1.4634 1.49 -- 146 2767 0.119 0.1673 -- 100.0
X Ray Diffraction 1.49 1.5187 -- 145 2763 0.1088 0.1518 -- 100.0
X Ray Diffraction 1.5187 1.5497 -- 147 2788 0.1034 0.1372 -- 100.0
X Ray Diffraction 1.5497 1.5834 -- 145 2757 0.0979 0.1282 -- 100.0
X Ray Diffraction 1.5834 1.6202 -- 147 2789 0.0983 0.1315 -- 100.0
X Ray Diffraction 1.6202 1.6607 -- 146 2772 0.0984 0.1361 -- 100.0
X Ray Diffraction 1.6607 1.7056 -- 145 2767 0.0996 0.1267 -- 100.0
X Ray Diffraction 1.7056 1.7558 -- 147 2794 0.1011 0.133 -- 100.0
X Ray Diffraction 1.7558 1.8125 -- 147 2782 0.1028 0.1489 -- 100.0
X Ray Diffraction 1.8125 1.8773 -- 146 2789 0.1042 0.1375 -- 100.0
X Ray Diffraction 1.8773 1.9524 -- 145 2753 0.1019 0.1169 -- 100.0
X Ray Diffraction 1.9524 2.0413 -- 147 2787 0.1033 0.1354 -- 100.0
X Ray Diffraction 2.0413 2.1489 -- 147 2786 0.1042 0.1443 -- 100.0
X Ray Diffraction 2.1489 2.2835 -- 146 2776 0.1147 0.127 -- 100.0
X Ray Diffraction 2.2835 2.4598 -- 146 2785 0.1228 0.1486 -- 100.0
X Ray Diffraction 2.4598 2.7072 -- 148 2800 0.1304 0.1533 -- 100.0
X Ray Diffraction 2.7072 3.0988 -- 147 2797 0.1391 0.1343 -- 100.0
X Ray Diffraction 3.0988 3.9033 -- 147 2798 0.1521 0.1748 -- 100.0
X Ray Diffraction 3.9033 34.8232 -- 151 2856 0.1587 0.1635 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.6077
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_bond_d 0.007
f_chiral_restr 0.07
f_angle_d 1.2
f_dihedral_angle_d 10.775
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 246

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