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X-ray structure of Clostridium perfringens-specific amidase endolysin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LBA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 200 mM potassium bromide, 200 mM potassium thiocyanate, 0.1 M sodium acetate, 3 % w/v poly-gamma-glutamic acid, 5% w/v PEG 3350, pH 5.0)
Crystal Properties Matthews coefficient Solvent content 2.08 40.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.01 α = 90 b = 52.87 β = 90 c = 58.61 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 IMAGE PLATE RIGAKU 2018-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.65 18.36 99.7 0.045 21.1 6.37 19657
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 1.65 1.69 0.859 2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1LBA 1.65 18.36 18658 957 99.76 0.14009 0.13667 0.1366 0.2047 0.2049 RANDOM 30.658
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] -0.54 0.56 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.017 r_dihedral_angle_4_deg 22.692 r_dihedral_angle_3_deg 17.432 r_scangle_other 9.452 r_scbond_it 9.062 r_scbond_other 8.872 r_long_range_B_refined 8.662 r_long_range_B_other 8.657 r_dihedral_angle_1_deg 7.214 r_mcangle_other 5.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.017 r_dihedral_angle_4_deg 22.692 r_dihedral_angle_3_deg 17.432 r_scangle_other 9.452 r_scbond_it 9.062 r_scbond_other 8.872 r_long_range_B_refined 8.662 r_long_range_B_other 8.657 r_dihedral_angle_1_deg 7.214 r_mcangle_other 5.865 r_mcangle_it 5.862 r_rigid_bond_restr 5.743 r_mcbond_it 5.016 r_mcbond_other 5.011 r_angle_refined_deg 1.514 r_angle_other_deg 1.392 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1241 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing