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Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with penicillin V
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JBF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 0.2 M NaCl, 0.1 M Bis-Tris, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.62 53.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.723 α = 90 b = 70.019 β = 96.93 c = 114.625 γ = 90
Symmetry Space Group P 1 21 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 CCD MARMOSAIC 225 mm CCD beryllium lenses 2013-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.85 30 99.8 0.07 17.7 3.8 89289 89289 -3 36.1
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 1.85 1.88 97.7 0.46 2.7 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 4JBF 1.85 30 84846 84846 4423 99.58 0.17631 0.17479 0.1798 0.20568 0.2101 RANDOM 36.064
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] 4.26 2.13 -3.57 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.776 r_dihedral_angle_3_deg 10.987 r_dihedral_angle_4_deg 10.486 r_long_range_B_refined 8.009 r_long_range_B_other 7.911 r_scangle_other 5.741 r_scbond_it 4.19 r_scbond_other 4.189 r_mcangle_it 3.849 r_mcangle_other 3.849
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.776 r_dihedral_angle_3_deg 10.987 r_dihedral_angle_4_deg 10.486 r_long_range_B_refined 8.009 r_long_range_B_other 7.911 r_scangle_other 5.741 r_scbond_it 4.19 r_scbond_other 4.189 r_mcangle_it 3.849 r_mcangle_other 3.849 r_dihedral_angle_1_deg 3.316 r_mcbond_it 2.731 r_mcbond_other 2.729 r_angle_refined_deg 1.82 r_angle_other_deg 0.894 r_chiral_restr 0.108 r_gen_planes_refined 0.018 r_bond_refined_d 0.014 r_gen_planes_other 0.014 r_bond_other_d 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 6012 Nucleic Acid Atoms Solvent Atoms 580 Heterogen Atoms 48
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling