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Endolysin from bacteriophage Enc34, catalytic domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Enc34 ORF39-SeMet
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 293 0.1 M phosphate/citrate, 0.2 M sodium chloride, 20% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 1.99 38.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.304 α = 90 b = 128.993 β = 90 c = 36.279 γ = 90
Symmetry Space Group P 21 21 2
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 EIGER X 16M 2020-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9763 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.6 45.89 100 0.168 0.175 0.996 9.9 12.156 41411 30.667
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 100 1.525 1.597 0.768 2.03 11.394
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 Enc34 ORF39-SeMet 1.6 45.89 39341 2071 99.98 0.179 0.1774 0.1892 0.2091 0.223 RANDOM 24.451
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] 0.21 0.78 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.024 r_dihedral_angle_4_deg 13.489 r_dihedral_angle_3_deg 12.756 r_dihedral_angle_1_deg 6.104 r_angle_refined_deg 1.519 r_angle_other_deg 1.422 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.024 r_dihedral_angle_4_deg 13.489 r_dihedral_angle_3_deg 12.756 r_dihedral_angle_1_deg 6.104 r_angle_refined_deg 1.519 r_angle_other_deg 1.422 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2591 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction