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Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with dicloxacillin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QJG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2 M Tri-Sodium Citrate, 0.1 M Tris, 15% PEG400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.65 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.611 α = 90 b = 69.882 β = 96.87 c = 114.251 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 1.84 30 99.9 0.08 22 3.8 91253 91253 -3 40.7
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 1.84 1.87 99.8 0.64 2 3.7 4542
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 4QJG 1.84 30 85416 85416 4501 98.19 0.15717 0.15541 0.1664 0.19183 0.2004 RANDOM 41.516
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] -0.29 -0.27 0.4 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.134 r_dihedral_angle_4_deg 14.769 r_dihedral_angle_3_deg 13.128 r_long_range_B_refined 7.864 r_long_range_B_other 7.791 r_dihedral_angle_1_deg 6.417 r_scangle_other 4.694 r_scbond_it 3.184 r_scbond_other 3.184 r_mcangle_it 2.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.134 r_dihedral_angle_4_deg 14.769 r_dihedral_angle_3_deg 13.128 r_long_range_B_refined 7.864 r_long_range_B_other 7.791 r_dihedral_angle_1_deg 6.417 r_scangle_other 4.694 r_scbond_it 3.184 r_scbond_other 3.184 r_mcangle_it 2.866 r_mcangle_other 2.866 r_mcbond_it 1.959 r_mcbond_other 1.959 r_angle_refined_deg 1.744 r_angle_other_deg 0.802 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 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 5950 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 105
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling