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Crystal structure of DHQ1 from Salmonella typhi covalently modified by ligand 1
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 24% PEG 2000 MME, 100 mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.16 43.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.878 α = 92.26 b = 43.844 β = 93.05 c = 73.261 γ = 119.25
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 1.14 38.14 88.6 0.071 0.101 0.071 0.996 6.3 1.8 150270 12.4
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) Redundancy Number Unique Reflections (All) 1 1.14 1.2 87.6 0.67 0.948 0.67 0.61 1.4 1.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4UIO 1.14 38.14 142383 7885 88.62 0.15264 0.151 0.1588 0.18242 0.1918 RANDOM 13.783
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 -1.21 0.65 0.74 0.57 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.709 r_sphericity_free 28.754 r_sphericity_bonded 13.357 r_dihedral_angle_4_deg 13.064 r_dihedral_angle_3_deg 12.237 r_dihedral_angle_1_deg 5.811 r_long_range_B_refined 3.391 r_long_range_B_other 2.839 r_scangle_other 2.102 r_scbond_it 1.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.709 r_sphericity_free 28.754 r_sphericity_bonded 13.357 r_dihedral_angle_4_deg 13.064 r_dihedral_angle_3_deg 12.237 r_dihedral_angle_1_deg 5.811 r_long_range_B_refined 3.391 r_long_range_B_other 2.839 r_scangle_other 2.102 r_scbond_it 1.628 r_scbond_other 1.628 r_mcangle_it 1.563 r_mcangle_other 1.563 r_angle_refined_deg 1.498 r_rigid_bond_restr 1.325 r_mcbond_it 1.237 r_mcbond_other 1.223 r_angle_other_deg 0.958 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3872 Nucleic Acid Atoms Solvent Atoms 703 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing