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MurT/GatD peptidoglycan amidotransferase complex from Streptococcus pneumoniae R6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 293.15 0.2 M tri-sodium citrate pH 6.1
14% PEG 3350
4 mM NiSO4
Crystal Properties Matthews coefficient Solvent content 2.84 56.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 288.43 α = 90 b = 288.43 β = 90 c = 115.1 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 193.15 PIXEL DECTRIS PILATUS3 2M 2014-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96500 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3 50 96.2 0.058 15.4 3 68725
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.18 96.6 0.447 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 SIRAS THROUGHOUT 3 50 61871 6854 96.16 0.19315 0.18923 0.2049 0.22809 0.2399 RANDOM 86.337
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] -2.67 -1.33 -2.67 8.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.534 r_dihedral_angle_4_deg 19.381 r_dihedral_angle_3_deg 16.33 r_long_range_B_refined 11.634 r_long_range_B_other 11.634 r_scangle_other 8.916 r_mcangle_it 8.676 r_mcangle_other 8.676 r_dihedral_angle_1_deg 6.833 r_scbond_it 5.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.534 r_dihedral_angle_4_deg 19.381 r_dihedral_angle_3_deg 16.33 r_long_range_B_refined 11.634 r_long_range_B_other 11.634 r_scangle_other 8.916 r_mcangle_it 8.676 r_mcangle_other 8.676 r_dihedral_angle_1_deg 6.833 r_scbond_it 5.784 r_scbond_other 5.779 r_mcbond_it 5.719 r_mcbond_other 5.718 r_angle_refined_deg 1.544 r_angle_other_deg 0.994 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 19687 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling SHARP phasing