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Crystal structure of the Klebsiella phage KP34p57 capsular depolymerase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 0.04 M cytric acid, 0.06 M bis-tris propane, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.35 47.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.34 α = 90 b = 140.985 β = 102.633 c = 81.925 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 2M 2021-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.987 ESRF BM30A
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 2 30 87.1 0.11 14.2 4.1 203918
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 2.2 2.25 91.3 0.41
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 SAD FREE R-VALUE 2 15 48807 746 78.471 0.205 0.2043 0.2111 0.2473 0.2532 30.55
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] 0.081 0.038 -0.066 -0.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.13 r_dihedral_angle_4_deg 15.091 r_dihedral_angle_3_deg 13.9 r_dihedral_angle_1_deg 8.719 r_lrange_it 5.83 r_lrange_other 5.767 r_scangle_it 3.563 r_scangle_other 3.563 r_mcangle_it 3.323 r_mcangle_other 3.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.13 r_dihedral_angle_4_deg 15.091 r_dihedral_angle_3_deg 13.9 r_dihedral_angle_1_deg 8.719 r_lrange_it 5.83 r_lrange_other 5.767 r_scangle_it 3.563 r_scangle_other 3.563 r_mcangle_it 3.323 r_mcangle_other 3.323 r_scbond_it 2.432 r_scbond_other 2.432 r_mcbond_it 2.326 r_mcbond_other 2.324 r_angle_refined_deg 1.529 r_angle_other_deg 1.257 r_xyhbond_nbd_refined 0.215 r_symmetry_nbd_other 0.194 r_nbd_refined 0.19 r_nbd_other 0.187 r_nbtor_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.151 r_symmetry_nbd_refined 0.133 r_symmetry_xyhbond_nbd_other 0.108 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.062 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 6480 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing RESOLVE model building