4EVU

Crystal structure of C-terminal domain of putative periplasmic protein ydgH from S. enterica


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62950.1 M Na Citrate , 0.2 M K/Na tartrate, 1.9 M (NH4)2SO4, 5% Glycerol, 1/210 trypsin, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2946.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.079α = 90
b = 52.521β = 109.38
c = 39.139γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2011-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97935APS19-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
11.455099.80.07925.23.72643226374-317.2
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)
11.451.481000.5762.23.61279

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 DIFFRACTIONSADTHROUGHOUT1.4536.922633026330127199.210.134370.134370.132570.17157RANDOM15.404
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]
0.08-2.930.26-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.656
r_dihedral_angle_3_deg13.936
r_dihedral_angle_4_deg12.726
r_scangle_it6.257
r_dihedral_angle_1_deg6.25
r_scbond_it4.185
r_mcangle_it3.259
r_mcbond_it1.979
r_rigid_bond_restr1.622
r_angle_refined_deg1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.656
r_dihedral_angle_3_deg13.936
r_dihedral_angle_4_deg12.726
r_scangle_it6.257
r_dihedral_angle_1_deg6.25
r_scbond_it4.185
r_mcangle_it3.259
r_mcbond_it1.979
r_rigid_bond_restr1.622
r_angle_refined_deg1.45
r_angle_other_deg0.886
r_mcbond_other0.549
r_chiral_restr0.096
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1071
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms11

Software

Software
Software NamePurpose
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing