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Structure of the Pseudomonas aeruginosa bacteriophage JG004 endolysin Pae87, apo form.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NM7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 294 20% (w/v) PEG 8000, 0.1 M CHES-NaOH, 20 mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.04 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.247 α = 90 b = 68.085 β = 90 c = 93.1 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 PIXEL DECTRIS PILATUS 6M 2019-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.5 59.25 99.7 0.183 0.202 0.083 0.991 6 5.7 13640 31.796
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 99.1 0.99 1.087 0.444 0.86 2.1 5.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5NM7 2.5 55.018 13599 658 99.743 0.225 0.2222 0.2254 0.2779 0.2765 56.402
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] -3.567 -2.533 6.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.684 r_dihedral_angle_4_deg 17.027 r_dihedral_angle_3_deg 11.734 r_dihedral_angle_1_deg 4.813 r_lrange_it 4.214 r_lrange_other 4.214 r_mcangle_it 2.011 r_mcangle_other 2.011 r_scangle_it 1.533 r_scangle_other 1.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.684 r_dihedral_angle_4_deg 17.027 r_dihedral_angle_3_deg 11.734 r_dihedral_angle_1_deg 4.813 r_lrange_it 4.214 r_lrange_other 4.214 r_mcangle_it 2.011 r_mcangle_other 2.011 r_scangle_it 1.533 r_scangle_other 1.533 r_mcbond_it 1.129 r_mcbond_other 1.127 r_angle_refined_deg 1.121 r_angle_other_deg 1.037 r_scbond_it 0.825 r_scbond_other 0.825 r_nbd_refined 0.158 r_nbtor_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.15 r_symmetry_nbd_other 0.147 r_xyhbond_nbd_refined 0.121 r_symmetry_nbd_refined 0.113 r_nbd_other 0.112 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.033 r_chiral_restr_other 0.028 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2964 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing