3KNZ

Crystal structure of Putative sugar binding protein (NP_459565.1) from Salmonella typhimurium LT2 at 2.50 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527737.1000% 2-ethoxyethanol, 0.0500M calcium acetate, 0.1M Imidazole pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.362.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.028α = 90
b = 173.344β = 90
c = 208.574γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2009-03-20MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91837,0.97934,0.97922SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.529.90799.90.1230.1239.63.811341248.836
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.561000.810.811.63.88264

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.529.907113329567299.970.2050.2030.232RANDOM27.788
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.490.83-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.974
r_dihedral_angle_4_deg11.969
r_dihedral_angle_3_deg10.066
r_scangle_it4.254
r_scbond_it2.956
r_dihedral_angle_1_deg2.453
r_mcangle_it1.339
r_angle_refined_deg1.148
r_angle_other_deg0.774
r_mcbond_it0.634
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.974
r_dihedral_angle_4_deg11.969
r_dihedral_angle_3_deg10.066
r_scangle_it4.254
r_scbond_it2.956
r_dihedral_angle_1_deg2.453
r_mcangle_it1.339
r_angle_refined_deg1.148
r_angle_other_deg0.774
r_mcbond_it0.634
r_mcbond_other0.167
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14786
Nucleic Acid Atoms
Solvent Atoms431
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SOLVEphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction