☰ Navigation Tabs
Crystal structure of endolysin gp46 from Pseudomonas aeruginosa bacteriophage vB_PaeM_KTN6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OK7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 10 mM HEPES-NaOH pH 7.0; 10 mM trisodium citrate; 16% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.37 48.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.796 α = 90 b = 43.201 β = 90 c = 126.181 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 2017-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97929 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.39 43.2 99.9 0.059 0.026 0.999 15.8 6.4 46757 17.995
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.39 1.47 99.7 1.002 0.425 0.695 1.8 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.391 40.003 46682 2227 99.767 0.128 0.1263 0.1263 0.1641 0.1639 27.118
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] -0.292 0.645 -0.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.048 r_dihedral_angle_4_deg 20.032 r_dihedral_angle_3_deg 11.992 r_dihedral_angle_1_deg 6.376 r_lrange_it 4.688 r_scangle_it 4.432 r_scangle_other 4.43 r_lrange_other 4.394 r_scbond_it 3.673 r_scbond_other 3.671
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.048 r_dihedral_angle_4_deg 20.032 r_dihedral_angle_3_deg 11.992 r_dihedral_angle_1_deg 6.376 r_lrange_it 4.688 r_scangle_it 4.432 r_scangle_other 4.43 r_lrange_other 4.394 r_scbond_it 3.673 r_scbond_other 3.671 r_mcangle_it 2.942 r_mcangle_other 2.941 r_mcbond_it 2.363 r_mcbond_other 2.357 r_rigid_bond_restr 1.76 r_angle_other_deg 1.457 r_angle_refined_deg 1.419 r_nbd_other 0.258 r_symmetry_nbd_refined 0.241 r_nbd_refined 0.211 r_symmetry_nbd_other 0.17 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.102 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1686 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing