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Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with cefapirin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N1X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.075 M HEPES Sodium Salt, 1.125 M Lithium sulfate, 25% Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.633 α = 90 b = 119.836 β = 90 c = 82.544 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 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 2.44 30 99.9 0.085 19.2 4.9 37197 37197 -3 56.2
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 2.44 2.49 99.7 0.6 2.6 4.9 1827
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 4N1X 2.44 30 35300 35300 1858 99.68 0.17364 0.1706 0.1768 0.23068 0.2285 RANDOM 48.212
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] -0.14 -0.43 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.839 r_dihedral_angle_3_deg 16.318 r_dihedral_angle_4_deg 15.882 r_dihedral_angle_1_deg 6.568 r_long_range_B_refined 6.373 r_long_range_B_other 6.355 r_scangle_other 4.804 r_scbond_it 3.593 r_scbond_other 3.538 r_mcangle_it 3.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.839 r_dihedral_angle_3_deg 16.318 r_dihedral_angle_4_deg 15.882 r_dihedral_angle_1_deg 6.568 r_long_range_B_refined 6.373 r_long_range_B_other 6.355 r_scangle_other 4.804 r_scbond_it 3.593 r_scbond_other 3.538 r_mcangle_it 3.344 r_mcangle_other 3.344 r_mcbond_it 2.191 r_mcbond_other 2.189 r_angle_refined_deg 1.64 r_angle_other_deg 0.796 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5826 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 67
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling