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Crystal structure of the modular Cpl-1 endolysin complexed with a peptidoglycan analogue (E94Q mutant in complex with a disaccharide- 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 3.18 61.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.23 α = 90 b = 95.59 β = 90 c = 129.27 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 1.65 64.55 96.3 0.12 3.3 5.4 47836 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 1.84 1.97 81.6 0.46 0.9 2.9
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 PDB ENTRY 1H09 1.84 64.55 38759 2960 96.12 0.18053 0.18053 0.1903 0.2152 0.2187 RANDOM 23.017
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] -1.59 1.43 0.15
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 4.103 c_scbond_it 2.655 c_mcangle_it 2.092 c_angle_deg 1.565 c_mcbond_it 1.19 c_bond_d 0.017 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 4.103 c_scbond_it 2.655 c_mcangle_it 2.092 c_angle_deg 1.565 c_mcbond_it 1.19 c_bond_d 0.017 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 333 Heterogen Atoms 90
Software Software Software Name Purpose CNS refinement MOSFLM data reduction SCALA data scaling MOLREP phasing