1TO3

Structure of yiht from Salmonella typhimurium


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42932% PEG 4000, 0.1M Cacodylate pH 6.5, 1.5M NaKPhosphate pH 8.5, 8% Glycerol; Cryoprotectant - 2% PEG 4000, 0.1M Cacodylate pH 6.5, 1.5M NaKPhosphate pH 8.5, 30% Glycerol, 1M NaBr, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.8767.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.144α = 90
b = 141.144β = 90
c = 102.726γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHVertical and horizontal focusing mirrors2003-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.979APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.72099.20.1239.45.41442714427-361
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.72.899.60.3244.14

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.720-3143921439272199.230.180180.180180.178670.20825RANDOM40.502
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]
-1.78-1.783.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.692
r_dihedral_angle_3_deg17.564
r_dihedral_angle_4_deg16.662
r_dihedral_angle_1_deg5.434
r_scangle_it2.319
r_scbond_it1.526
r_angle_refined_deg1.467
r_mcangle_it0.956
r_angle_other_deg0.836
r_mcbond_it0.831
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.692
r_dihedral_angle_3_deg17.564
r_dihedral_angle_4_deg16.662
r_dihedral_angle_1_deg5.434
r_scangle_it2.319
r_scbond_it1.526
r_angle_refined_deg1.467
r_mcangle_it0.956
r_angle_other_deg0.836
r_mcbond_it0.831
r_symmetry_vdw_other0.268
r_nbd_refined0.222
r_nbd_other0.195
r_symmetry_hbond_refined0.191
r_xyhbond_nbd_refined0.185
r_symmetry_vdw_refined0.185
r_mcbond_other0.119
r_nbtor_other0.091
r_chiral_restr0.076
r_bond_refined_d0.014
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2218
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing