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Staphyloferrin B precursor biosynthetic enzyme SbnA bound to PLP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1 M Tris, pH 8.5, 0.2 M MgCl2, 20-25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.04 39.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.08 α = 90 b = 115.828 β = 90 c = 45.138 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 CCD RAYONIX MX300HE Vertical Focusing Mirror: ultra-low expansion (ULE) titanium siliicate flat mirror with Pt, Uncoated, and Pd strips 2010-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97952 CLSI 08ID-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 1.45 50 97.3 0.055 13 5.9 51631
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 1.45 1.5 94.7 0.413 5.6 4954
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.45 50 48724 2598 96.82 0.1265 0.1239 0.1753 0.1774 RANDOM 18.813
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] -0.25 0.59 -0.35
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.449 r_dihedral_angle_2_deg 36.923 r_sphericity_bonded 16.278 r_dihedral_angle_4_deg 15.178 r_dihedral_angle_3_deg 12.462 r_dihedral_angle_1_deg 5.436 r_scbond_it 3.354 r_mcangle_it 3.327 r_rigid_bond_restr 3.049 r_mcbond_it 2.627
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.449 r_dihedral_angle_2_deg 36.923 r_sphericity_bonded 16.278 r_dihedral_angle_4_deg 15.178 r_dihedral_angle_3_deg 12.462 r_dihedral_angle_1_deg 5.436 r_scbond_it 3.354 r_mcangle_it 3.327 r_rigid_bond_restr 3.049 r_mcbond_it 2.627 r_angle_refined_deg 1.515 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2456 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 16
Software Software Software Name Purpose HKL-2000 data scaling PHENIX phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction