4OD6

Structure of Smr domain of MutS2 from Deinococcus radiodurans, Mn2+ soaked


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Crystal Formed Spontaneously in Protein Solution Stored at 4 Degree
pH 8.8
Temperature 297.0
Details 30mM NaCl and 20mM Tris-HCl, soaked in 5mM MnCl2 before x-ray data collection, pH 8.8, crystal formed spontaneously in protein solution stored at 4 degree, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 31.12 α = 90
b = 46.64 β = 90
c = 49.26 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-06-02
Diffraction Radiation
Monochromator Protocol
silicon 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.97930 SSRF BL17U

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
1.2 30 98.3 -- -- -- -- 23113 22713 -- -3.0 --
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)
1.199 1.23 96.7 -- -- -- -- --

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 1.199 26.31 -- 1.34 23117 22694 1170 98.17 -- 0.1834 0.1821 0.2089 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 1.199 1.2535 -- 162 2592 0.289 0.36 -- 98.0
X Ray Diffraction 1.2535 1.3196 -- 156 2659 0.2565 0.2862 -- 99.0
X Ray Diffraction 1.3196 1.4023 -- 132 2729 0.1809 0.219 -- 100.0
X Ray Diffraction 1.4023 1.5106 -- 141 2705 0.1858 0.2445 -- 99.0
X Ray Diffraction 1.5106 1.6626 -- 150 2703 0.1503 0.1807 -- 100.0
X Ray Diffraction 1.6626 1.9031 -- 132 2716 0.1595 0.1803 -- 99.0
X Ray Diffraction 1.9031 2.3974 -- 142 2651 0.182 0.1926 -- 95.0
X Ray Diffraction 2.3974 26.3159 -- 155 2769 0.1701 0.1838 -- 96.0
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.093
f_bond_d 0.019
f_angle_d 1.849
f_dihedral_angle_d 13.04
f_plane_restr 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 635
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 119

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.8.4_1496)
XDS data reduction
XDS data scaling