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Crystal structure of DHQ1 from Salmonella typhi covalently modified by ligand 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UIO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 26% PEG 2000 MME, 100mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.06 40.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.726 α = 90 b = 114.632 β = 90 c = 42.55 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2017-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97918 ALBA XALOC
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.04 46.73 99.9 0.062 0.068 0.028 0.999 16.9 10.2 109612 10.3
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) Redundancy Number Unique Reflections (All) 1 1.04 1.1 99.5 0.777 0.893 0.43 0.767 2.2 7.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4UIO 1.04 46.73 104069 5426 99.91 0.12471 0.12366 0.14436 0.1572 RANDOM 15.634
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] -0.24 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.245 r_sphericity_free 23.255 r_dihedral_angle_4_deg 14.39 r_dihedral_angle_3_deg 11.899 r_sphericity_bonded 7.816 r_dihedral_angle_1_deg 5.813 r_long_range_B_refined 3.24 r_long_range_B_other 2.373 r_scangle_other 1.663 r_angle_refined_deg 1.466
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.245 r_sphericity_free 23.255 r_dihedral_angle_4_deg 14.39 r_dihedral_angle_3_deg 11.899 r_sphericity_bonded 7.816 r_dihedral_angle_1_deg 5.813 r_long_range_B_refined 3.24 r_long_range_B_other 2.373 r_scangle_other 1.663 r_angle_refined_deg 1.466 r_scbond_it 1.342 r_scbond_other 1.342 r_mcangle_it 1.198 r_mcangle_other 1.198 r_rigid_bond_restr 1.105 r_angle_other_deg 0.96 r_mcbond_it 0.884 r_mcbond_other 0.868 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1936 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing