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Crystal structure of SbnH in complex with citrate, a PLP-dependent decarboxylase in Staphyloferrin B biothesynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J66
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 290 0.2 M NaAC, 50mM Bis-Tris pH6.0, 23% PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.89 57.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.291 α = 90 b = 79.585 β = 102.48 c = 111.656 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 16M 2018-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9791 SSRF BL17U
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 1.76 50 95.1 0.088 21.6 3.4 139539
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 1.76 1.82 0.49
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 2J66 1.76 50.01 132551 6986 94.6 0.1697 0.1687 0.1783 0.188 0.1953 RANDOM 25.812
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] 0.2 0.54 1.27 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.007 r_dihedral_angle_4_deg 15.073 r_dihedral_angle_3_deg 11.493 r_dihedral_angle_1_deg 6.165 r_long_range_B_other 3.833 r_long_range_B_refined 3.832 r_scangle_other 2.493 r_mcangle_it 1.754 r_mcangle_other 1.754 r_scbond_it 1.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.007 r_dihedral_angle_4_deg 15.073 r_dihedral_angle_3_deg 11.493 r_dihedral_angle_1_deg 6.165 r_long_range_B_other 3.833 r_long_range_B_refined 3.832 r_scangle_other 2.493 r_mcangle_it 1.754 r_mcangle_other 1.754 r_scbond_it 1.535 r_scbond_other 1.524 r_angle_refined_deg 1.215 r_mcbond_it 1.092 r_mcbond_other 1.091 r_angle_other_deg 0.892 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9177 Nucleic Acid Atoms Solvent Atoms 500 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing