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Crystal structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum DSM 20469
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2 M Calcium Chloride, 0.1 M HEPES, 20% PEG6000, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.98 37.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.68 α = 90 b = 45.51 β = 102.78 c = 71.29 γ = 90
Symmetry Space Group C 1 2 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 3.0 Undulator 2013-10-21 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 29.17 99 0.09 9.8 5.6 32538 32538 -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 2 2.05 95.6 0.052 2.5 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2 29.17 30883 30883 1646 98.94 0.18223 0.17947 0.1939 0.23269 0.2394 RANDOM 48.813
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] -4.36 1.86 3.7 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.197 r_dihedral_angle_4_deg 16.628 r_dihedral_angle_3_deg 11.566 r_long_range_B_refined 10.066 r_long_range_B_other 10.053 r_scangle_other 8.333 r_scbond_it 5.957 r_scbond_other 5.956 r_mcangle_it 5.057 r_mcangle_other 5.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.197 r_dihedral_angle_4_deg 16.628 r_dihedral_angle_3_deg 11.566 r_long_range_B_refined 10.066 r_long_range_B_other 10.053 r_scangle_other 8.333 r_scbond_it 5.957 r_scbond_other 5.956 r_mcangle_it 5.057 r_mcangle_other 5.056 r_mcbond_it 4.065 r_mcbond_other 4.061 r_dihedral_angle_1_deg 3.501 r_angle_refined_deg 2.107 r_angle_other_deg 0.908 r_chiral_restr 0.135 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 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 3178 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 1
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement Aimless data scaling