6H5J

Crystal structure of DHQ1 from Salmonella typhi covalently modified by ligand 4


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.629324% PEG 4000, 0.1 M citrate/phosphate
Crystal Properties
Matthews coefficientSolvent content
2.0439.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.498α = 90
b = 46.598β = 90
c = 114.491γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97925ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.442.5389.40.040.0440.0170.99910.86.14071713.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4852.80.3870.4370.1950.91824.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.442.5338638204089.030.128690.126160.17754RANDOM17.308
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]
-0.540.270.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.521
r_sphericity_free26.327
r_dihedral_angle_4_deg15.75
r_dihedral_angle_3_deg12.55
r_sphericity_bonded9.168
r_dihedral_angle_1_deg5.638
r_rigid_bond_restr3.396
r_angle_refined_deg1.596
r_angle_other_deg0.878
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.521
r_sphericity_free26.327
r_dihedral_angle_4_deg15.75
r_dihedral_angle_3_deg12.55
r_sphericity_bonded9.168
r_dihedral_angle_1_deg5.638
r_rigid_bond_restr3.396
r_angle_refined_deg1.596
r_angle_other_deg0.878
r_chiral_restr0.101
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_symmetry_metal_ion_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_nbd_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_nbd_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_nbtor_refined
r_nbtor_other
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1936
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing