X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details 0.2 M sodium formate, 0.1M bicine, pH 8.5; 20% w/v PEG MME 5000, and 0.5-1 mM c-di-GMP, 20% xylitol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.38 α = 90
b = 90.22 β = 115.49
c = 82.75 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 ADSC QUANTUM 210 -- 2011-11-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE A1 0.977 CHESS A1

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
2.6 50 99.9 0.062 -- -- 3.8 -- 31030 -- -- 69.27
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)
2.64 2.73 100.0 0.66 -- -- 3.8 --

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 2.61 33.77 -- 1.34 -- 30983 1999 98.54 -- 0.2005 0.1973 0.2485 --
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 2.61 2.67 -- 122 1695 0.311 0.3877 -- 81.01
X Ray Diffraction 2.67 2.75 -- 139 2058 0.2794 0.3605 -- 99.91
X Ray Diffraction 2.75 2.83 -- 148 2117 0.2635 0.3132 -- 99.87
X Ray Diffraction 2.83 2.92 -- 137 2067 0.2596 0.3051 -- 99.82
X Ray Diffraction 2.92 3.02 -- 150 2076 0.2395 0.3238 -- 99.96
X Ray Diffraction 3.02 3.14 -- 136 2117 0.2527 0.3204 -- 99.87
X Ray Diffraction 3.14 3.29 -- 146 2081 0.2514 0.3284 -- 99.91
X Ray Diffraction 3.29 3.46 -- 144 2109 0.2255 0.3193 -- 100.0
X Ray Diffraction 3.46 3.67 -- 147 2086 0.2049 0.2616 -- 99.96
X Ray Diffraction 3.67 3.96 -- 151 2102 0.1914 0.2129 -- 99.91
X Ray Diffraction 3.96 4.36 -- 134 2104 0.173 0.2231 -- 99.82
X Ray Diffraction 4.36 4.98 -- 147 2108 0.1647 0.2221 -- 99.91
X Ray Diffraction 4.98 6.27 -- 149 2103 0.2023 0.2362 -- 100.0
X Ray Diffraction 6.27 33.77 -- 149 2161 0.1602 0.2004 -- 99.74
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 81.02
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.0022
f_dihedral_angle_d 16.7263
f_plane_restr 0.0026
f_angle_d 0.6618
f_chiral_restr 0.0434
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6425
Nucleic Acid Atoms 0
Heterogen Atoms 186
Solvent Atoms 40

Software

Software
Software Name Purpose
PHENIX refinement version: 1.13_2998
SCALEPACK data scaling
PDB_EXTRACT data extraction version: 3.25
HKL-2000 data reduction
PHENIX phasing