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Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with cephalothin
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 6.5 293 0.2 M Potassium thiocyanate, 0.1 M Bis-Tris propane, 20 % PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.71 54.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.553 α = 90 b = 70.002 β = 96.76 c = 115.233 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 2 30 99.2 0.085 19.7 3.6 72944 72944 -3 43
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 2.03 91.7 0.59 2.1 3.1
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 30 69023 69023 3668 98.53 0.18089 0.17903 0.1862 0.21662 0.2209 RANDOM 46.261
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] -0.8 -0.56 0.96 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.643 r_dihedral_angle_4_deg 14.456 r_dihedral_angle_3_deg 14.324 r_long_range_B_other 7.562 r_long_range_B_refined 7.561 r_dihedral_angle_1_deg 6.505 r_scangle_other 3.78 r_mcangle_it 2.66 r_mcangle_other 2.66 r_scbond_it 2.537
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.643 r_dihedral_angle_4_deg 14.456 r_dihedral_angle_3_deg 14.324 r_long_range_B_other 7.562 r_long_range_B_refined 7.561 r_dihedral_angle_1_deg 6.505 r_scangle_other 3.78 r_mcangle_it 2.66 r_mcangle_other 2.66 r_scbond_it 2.537 r_scbond_other 2.534 r_mcbond_it 1.782 r_mcbond_other 1.701 r_angle_refined_deg 1.689 r_angle_other_deg 0.947 r_chiral_restr 0.092 r_bond_refined_d 0.014 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 5938 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 88
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling