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Catalytic domain of CD27L endolysin targeting Clostridia Difficile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XOV PDB entry 1XOV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 292 0.1 M Tris-HCl, 0.2 M LiSO4, 20 % PEG 4000, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.27 45.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.507 α = 101.72 b = 69.737 β = 102 c = 78.818 γ = 105.24
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 2010-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 EMBL/DESY, HAMBURG X12
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 1.87 20 88.3 0.137 8.9 1.8 58273 50589
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 1.87 1.9 69.8 0.31 2.3 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1XOV 2 20 41298 2166 91.18 0.18698 0.18383 0.1916 0.24571 0.2316 RANDOM 15.946
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] -0.18 -0.81 -0.38 -0.99 -0.11 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.821 r_dihedral_angle_4_deg 18.918 r_dihedral_angle_3_deg 11.87 r_dihedral_angle_1_deg 5.62 r_scangle_it 1.62 r_scbond_it 0.988 r_angle_refined_deg 0.983 r_angle_other_deg 0.749 r_mcangle_it 0.602 r_mcbond_it 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.821 r_dihedral_angle_4_deg 18.918 r_dihedral_angle_3_deg 11.87 r_dihedral_angle_1_deg 5.62 r_scangle_it 1.62 r_scbond_it 0.988 r_angle_refined_deg 0.983 r_angle_other_deg 0.749 r_mcangle_it 0.602 r_mcbond_it 0.317 r_mcbond_other 0.063 r_chiral_restr 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5620 Nucleic Acid Atoms Solvent Atoms 1142 Heterogen Atoms 74
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling