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Crystal structure of SbnC in the biosynthesis of staphyloferrin B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.2 M tri-Lithium citrate, 22% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.98 69.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.81 α = 90 b = 151.319 β = 90 c = 197.08 γ = 90
Symmetry Space Group I 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 6M 2019-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.978763716744 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.6 50 100 0.029 20.7 13.1 64879
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.66 99.7 0.209 3.3 13.5
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 SAD THROUGHOUT 2.6 50 61810 3043 99.9 0.19745 0.19674 0.2068 0.2111 0.221 RANDOM 51.337
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] -0.99 3.6 -2.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.588 r_dihedral_angle_4_deg 17.431 r_dihedral_angle_3_deg 14.928 r_long_range_B_refined 6.623 r_long_range_B_other 6.623 r_dihedral_angle_1_deg 5.925 r_scangle_other 2.949 r_mcangle_it 2.899 r_mcangle_other 2.899 r_scbond_it 1.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.588 r_dihedral_angle_4_deg 17.431 r_dihedral_angle_3_deg 14.928 r_long_range_B_refined 6.623 r_long_range_B_other 6.623 r_dihedral_angle_1_deg 5.925 r_scangle_other 2.949 r_mcangle_it 2.899 r_mcangle_other 2.899 r_scbond_it 1.733 r_scbond_other 1.732 r_mcbond_it 1.702 r_mcbond_other 1.702 r_angle_refined_deg 1.197 r_angle_other_deg 1.154 r_chiral_restr 0.045 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9108 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling AutoSol phasing