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Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with nafcillin
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 6.5 293 0.2 M Sodium Iodide, 0.1 M Bis-Tris propane, 20 % PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.89 57.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.399 α = 90 b = 70.059 β = 96.97 c = 114.567 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 300 mm CCD MIRROR 2013-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.94 30 99.4 0.075 29.3 4.1 79452 79452 -3
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 1.94 1.97 94.4 0.61 2.2 3.7
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 1.94 30 75451 75451 3984 99.26 0.16322 0.1613 0.1701 0.19901 0.2047 RANDOM 50.549
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] 4.74 1.63 -5.67 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.752 r_dihedral_angle_4_deg 17.475 r_dihedral_angle_3_deg 13.61 r_long_range_B_refined 7.043 r_long_range_B_other 6.998 r_dihedral_angle_1_deg 6.398 r_scangle_other 4.058 r_mcangle_it 2.993 r_mcangle_other 2.993 r_scbond_it 2.793
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.752 r_dihedral_angle_4_deg 17.475 r_dihedral_angle_3_deg 13.61 r_long_range_B_refined 7.043 r_long_range_B_other 6.998 r_dihedral_angle_1_deg 6.398 r_scangle_other 4.058 r_mcangle_it 2.993 r_mcangle_other 2.993 r_scbond_it 2.793 r_scbond_other 2.793 r_mcbond_it 1.998 r_mcbond_other 1.998 r_angle_refined_deg 1.701 r_angle_other_deg 0.793 r_chiral_restr 0.156 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 5983 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 54
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling