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LysTt72, a lytic endopeptidase from Thermus thermophilus MAT72 phage vB_Tt72
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8S3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 20% v/v PEG 500 MME, 10% w/v PEG 20000, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulfate, 0.1 M 6.5 imidazole/MES monohydrate (acid) at pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.88 34.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.53 α = 90 b = 60.15 β = 90 c = 124.25 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-F focussing mirrors 2023-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9790 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.3 100 99.9 0.107 0.111 0.999 13.58 13 14096
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.44 99.3 1.652 1.725 0.848 1.42 12
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 2.301 62.125 14090 564 99.879 0.197 0.1927 0.205 0.2976 0.3011 72.882
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] 5.509 1.456 -6.965
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.06 r_lrange_it 15.958 r_lrange_other 15.956 r_dihedral_angle_6_deg 15.197 r_scangle_it 12.329 r_scangle_other 12.327 r_dihedral_angle_2_deg 10.628 r_mcangle_other 10.478 r_mcangle_it 10.466 r_scbond_it 8.489
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.06 r_lrange_it 15.958 r_lrange_other 15.956 r_dihedral_angle_6_deg 15.197 r_scangle_it 12.329 r_scangle_other 12.327 r_dihedral_angle_2_deg 10.628 r_mcangle_other 10.478 r_mcangle_it 10.466 r_scbond_it 8.489 r_scbond_other 8.469 r_dihedral_angle_1_deg 8.358 r_mcbond_it 7.687 r_mcbond_other 7.683 r_angle_refined_deg 1.909 r_angle_other_deg 0.632 r_xyhbond_nbd_refined 0.261 r_nbd_refined 0.239 r_nbd_other 0.229 r_symmetry_nbd_other 0.215 r_metal_ion_refined 0.209 r_nbtor_refined 0.202 r_symmetry_nbd_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.102 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.084 r_symmetry_xyhbond_nbd_other 0.012 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2837 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing