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Crystal structure of the modular Cpl-1 endolysin complexed with a peptidoglycan analogue (E94Q mutant in complex with a tetrasaccharide- pentapeptide)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H09 PDB ENTRY 1H09
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.16 61.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.52 α = 90 b = 97.39 β = 90 c = 127.14 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC CCD 2006-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.51 63.62 92.6 0.12 3.3 5.5 58301 1
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 1.69 1.81 71.4 0.5 1.1 3.4
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 1H09 1.69 63.25 47556 3644 92.33 0.18656 0.18656 0.2021 0.2203 0.2381 RANDOM 20.707
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] 0.67 -0.36 -0.31
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.946 c_scbond_it 2.546 c_mcangle_it 1.888 c_angle_deg 1.496 c_mcbond_it 1.058 c_bond_d 0.016 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.946 c_scbond_it 2.546 c_mcangle_it 1.888 c_angle_deg 1.496 c_mcbond_it 1.058 c_bond_d 0.016 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2763 Nucleic Acid Atoms Solvent Atoms 454 Heterogen Atoms 72
Software Software Software Name Purpose CNS refinement MOSFLM data reduction SCALA data scaling MOLREP phasing