6H5C

Crystal structure of DHQ1 from Salmonella typhi covalently modified by ligand 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729324% PEG 2000 MME, 100 mM HEPES
Crystal Properties
Matthews coefficientSolvent content
2.1643.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.878α = 92.26
b = 43.844β = 93.05
c = 73.261γ = 119.25
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97918ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.1438.1488.60.0710.1010.0710.9966.31.815027012.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.141.287.60.670.9480.670.611.41.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT4UIO1.1438.14142383788588.620.152640.1510.18242RANDOM13.783
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]
-1.02-1.210.650.740.570.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.709
r_sphericity_free28.754
r_sphericity_bonded13.357
r_dihedral_angle_4_deg13.064
r_dihedral_angle_3_deg12.237
r_dihedral_angle_1_deg5.811
r_long_range_B_refined3.391
r_long_range_B_other2.839
r_scangle_other2.102
r_scbond_it1.628
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.709
r_sphericity_free28.754
r_sphericity_bonded13.357
r_dihedral_angle_4_deg13.064
r_dihedral_angle_3_deg12.237
r_dihedral_angle_1_deg5.811
r_long_range_B_refined3.391
r_long_range_B_other2.839
r_scangle_other2.102
r_scbond_it1.628
r_scbond_other1.628
r_mcangle_it1.563
r_mcangle_other1.563
r_angle_refined_deg1.498
r_rigid_bond_restr1.325
r_mcbond_it1.237
r_mcbond_other1.223
r_angle_other_deg0.958
r_chiral_restr0.091
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_refined
r_symmetry_metal_ion_other
r_symmetry_vdw_other
r_metal_ion_other
r_metal_ion_refined
r_xyhbond_nbd_other
r_symmetry_hbond_refined
r_nbtor_other
r_scangle_it
r_nbtor_refined
r_nbd_other
r_nbd_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3872
Nucleic Acid Atoms
Solvent Atoms703
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing