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Native structure of the lytic CHAPK domain of the endolysin LysK from Staphylococcus aureus bacteriophage K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CT3 INTERMEDIATE MODEL BASED ON DERIVATIVE DATA, PDB ENTRY 4CT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 25 MM TRIS-HCL, 22% (W/V) POLYETHYLENE GLYCOL 8000, 0.1 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID-NAOH PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.3 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.22 α = 91.49 b = 61.47 β = 98.62 c = 73.13 γ = 89.99
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 ONE PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK-BAEZ GEOMETRY 2014-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 1.79 36.53 97.2 0.09 6.3 2 62028 14.5
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 1.79 1.88 94.3 0.25 2.9 1.9
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 INTERMEDIATE MODEL BASED ON DERIVATIVE DATA, PDB ENTRY 4CT3 1.79 32.85 59686 2338 97.17 0.17598 0.17486 0.1836 0.20106 0.2095 RANDOM, COPIED FROM DERIVATIVE DATA 18.402
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] -0.12 0.64 0.53 -0.52 -0.16 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.784 r_dihedral_angle_3_deg 12.098 r_dihedral_angle_4_deg 8.934 r_dihedral_angle_1_deg 5.974 r_scangle_it 3.016 r_mcangle_it 2.411 r_scbond_it 1.924 r_mcbond_it 1.499 r_mcbond_other 1.498 r_angle_refined_deg 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.784 r_dihedral_angle_3_deg 12.098 r_dihedral_angle_4_deg 8.934 r_dihedral_angle_1_deg 5.974 r_scangle_it 3.016 r_mcangle_it 2.411 r_scbond_it 1.924 r_mcbond_it 1.499 r_mcbond_other 1.498 r_angle_refined_deg 1.47 r_angle_other_deg 1.279 r_symmetry_hbond_refined 0.294 r_symmetry_vdw_refined 0.283 r_nbd_refined 0.275 r_symmetry_vdw_other 0.202 r_nbtor_refined 0.182 r_nbd_other 0.176 r_xyhbond_nbd_refined 0.149 r_metal_ion_refined 0.139 r_chiral_restr 0.086 r_nbtor_other 0.078 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.007 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5232 Nucleic Acid Atoms Solvent Atoms 741 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling