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Crystal structure of vancomycin-Zn(II)-citrate complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M di-ammonium hydrogen citrate salt and 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.31 62.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.038 α = 90 b = 57.481 β = 90 c = 21.638 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 S 6M 2015-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 0.95 37.31 98.2 0.052 30.1 9.9 19399
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.95 1 90.5 0.085 11.7 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 0.95 37.31 17433 1939 98.02 0.10616 0.1049 0.1118 0.11758 0.1264 RANDOM 5.921
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.787 r_sphericity_free 31.706 r_dihedral_angle_1_deg 14.756 r_rigid_bond_restr 6.937 r_dihedral_angle_3_deg 6.751 r_sphericity_bonded 5.603 r_angle_other_deg 4.925 r_angle_refined_deg 2.738 r_long_range_B_refined 2.247 r_long_range_B_other 1.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.787 r_sphericity_free 31.706 r_dihedral_angle_1_deg 14.756 r_rigid_bond_restr 6.937 r_dihedral_angle_3_deg 6.751 r_sphericity_bonded 5.603 r_angle_other_deg 4.925 r_angle_refined_deg 2.738 r_long_range_B_refined 2.247 r_long_range_B_other 1.321 r_scangle_other 1.038 r_scbond_other 0.911 r_scbond_it 0.908 r_mcangle_it 0.613 r_mcangle_other 0.608 r_mcbond_it 0.596 r_mcbond_other 0.588 r_chiral_restr 0.22 r_bond_refined_d 0.042 r_gen_planes_refined 0.041 r_bond_other_d 0.01 r_gen_planes_other 0.009 r_dihedral_angle_4_deg 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 160 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing