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 11 with the SMILES code CC1=CC(NC(=O)CCOC2=CC=CC=C2)=NO1

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.39 α = 90
b = 73.15 β = 109.85
c = 52.98 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 MARMOSAIC 225 mm CCD -- 2012-09-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.91842 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
1.45 42.69 98.4 0.069 -- -- 4.115 -- 57017 -- -3.0 9.67
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)
1.45 1.54 91.9 0.453 -- 2.8 -- --

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 1.449 36.869 -- 1.36 -- 57015 2851 98.58 -- 0.1431 0.1414 0.1743 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 1.4488 1.4737 -- 119 2271 0.1713 0.2326 -- 82.0
X Ray Diffraction 1.4737 1.5005 -- 132 2505 0.1607 0.2274 -- 92.0
X Ray Diffraction 1.5005 1.5294 -- 144 2734 0.1509 0.2166 -- 100.0
X Ray Diffraction 1.5294 1.5606 -- 144 2744 0.1373 0.1842 -- 100.0
X Ray Diffraction 1.5606 1.5945 -- 143 2719 0.132 0.2074 -- 100.0
X Ray Diffraction 1.5945 1.6316 -- 144 2733 0.1239 0.1766 -- 100.0
X Ray Diffraction 1.6316 1.6724 -- 146 2762 0.1204 0.1727 -- 100.0
X Ray Diffraction 1.6724 1.7177 -- 143 2730 0.1163 0.1801 -- 100.0
X Ray Diffraction 1.7177 1.7682 -- 143 2717 0.1156 0.1833 -- 100.0
X Ray Diffraction 1.7682 1.8253 -- 145 2751 0.1111 0.14 -- 100.0
X Ray Diffraction 1.8253 1.8905 -- 145 2750 0.1196 0.1661 -- 100.0
X Ray Diffraction 1.8905 1.9662 -- 144 2736 0.1213 0.1717 -- 100.0
X Ray Diffraction 1.9662 2.0557 -- 143 2727 0.1298 0.1592 -- 100.0
X Ray Diffraction 2.0557 2.164 -- 145 2737 0.1309 0.1697 -- 100.0
X Ray Diffraction 2.164 2.2996 -- 143 2734 0.1367 0.1734 -- 100.0
X Ray Diffraction 2.2996 2.4771 -- 145 2738 0.1441 0.1907 -- 100.0
X Ray Diffraction 2.4771 2.7263 -- 145 2759 0.1504 0.1802 -- 100.0
X Ray Diffraction 2.7263 3.1207 -- 145 2751 0.1591 0.1728 -- 100.0
X Ray Diffraction 3.1207 3.931 -- 144 2754 0.1641 0.1702 -- 100.0
X Ray Diffraction 3.931 36.8814 -- 149 2812 0.1525 0.155 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.7186
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_dihedral_angle_d 10.991
f_angle_d 1.161
f_bond_d 0.008
f_chiral_restr 0.069
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 224

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