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Catalytic domain of LytA, the major autolysin of Streptococcus pneumoniae, (C60A, H133A, C136A mutant) complexed with peptidoglycan fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 PEG 6000, 1M LiCl, 0.1M Tris HCl
Crystal Properties Matthews coefficient Solvent content 2.07 40.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.566 α = 90 b = 54.623 β = 90 c = 78.877 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2014-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972 ESRF ID23-1
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 1.05 45 99.8 0.094 10.2 5.9 90326
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 1.05 1.07 65.1 0.65 2.1 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4IVV 1.05 44.91 85673 4525 99.71 0.13477 0.13383 0.15273 0.1547 RANDOM 9.125
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] -0.07 0.11 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.802 r_sphericity_free 28.649 r_dihedral_angle_3_deg 9.567 r_dihedral_angle_4_deg 8.948 r_sphericity_bonded 6.284 r_dihedral_angle_1_deg 6.22 r_long_range_B_refined 2.334 r_long_range_B_other 1.705 r_scangle_other 1.586 r_rigid_bond_restr 1.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.802 r_sphericity_free 28.649 r_dihedral_angle_3_deg 9.567 r_dihedral_angle_4_deg 8.948 r_sphericity_bonded 6.284 r_dihedral_angle_1_deg 6.22 r_long_range_B_refined 2.334 r_long_range_B_other 1.705 r_scangle_other 1.586 r_rigid_bond_restr 1.514 r_angle_refined_deg 1.325 r_scbond_other 1.202 r_scbond_it 1.187 r_mcangle_other 1.077 r_mcangle_it 1.057 r_mcbond_it 0.865 r_angle_other_deg 0.826 r_mcbond_other 0.757 r_chiral_restr 0.241 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1488 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing