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Crystal structure of BshA from B. subtilis complexed with N-acetylglucosaminyl-malate and UMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 2% (v/v) tascimate, 6% (w/v) PEG-3400, 25 mM NaCl, 10 mM HEPES, 5 mM UDP-N-acetylglucosamine
Crystal Properties Matthews coefficient Solvent content 2.16 43.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.66 α = 90 b = 164.627 β = 90 c = 97.729 γ = 90
Symmetry Space Group C 2 2 21
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 MARMOSAIC 300 mm CCD 2014-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.078 APS 21-ID-D
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 2.15 93.73 100 0.093 15 9.6 40122
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 2.15 2.27 100 0.69 3.7 9.9
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 3MBO 2.15 82.31 38084 2010 99.96 0.1868 0.1843 0.1934 0.2341 0.2349 RANDOM 41.659
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] -0.15 -0.26 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.569 r_dihedral_angle_4_deg 18.877 r_dihedral_angle_3_deg 15.324 r_dihedral_angle_1_deg 6.809 r_mcangle_it 4.972 r_mcbond_it 3.475 r_mcbond_other 3.462 r_angle_refined_deg 1.823 r_angle_other_deg 0.841 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.569 r_dihedral_angle_4_deg 18.877 r_dihedral_angle_3_deg 15.324 r_dihedral_angle_1_deg 6.809 r_mcangle_it 4.972 r_mcbond_it 3.475 r_mcbond_other 3.462 r_angle_refined_deg 1.823 r_angle_other_deg 0.841 r_chiral_restr 0.102 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5555 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 72
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction SCALA data scaling XDS data scaling Coot model building