☰ Navigation Tabs
Crystal structure of PPK2 class III from Erysipelotrichaceae bacterium in complex with polyphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 285 MPD 10 %; NaOAc 0.1 M;NaCl 0.2 M; pH 5.40
Crystal Properties Matthews coefficient Solvent content 2.98 58.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.471 α = 90 b = 88.265 β = 101.151 c = 125.344 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M 2024-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.31 45.11 96.6 0.137 0.0525 0.996 9.03 6.81 72761 50.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.31 2.45 94.8 17.36 6.53 0.773 0.98 7.06
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 2.311 45.109 72669 3729 96.459 0.178 0.176 0.176 0.2127 0.2129 67.877
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] -1.021 3.467 0.562 -0.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.607 r_dihedral_angle_3_deg 15.553 r_lrange_it 10.683 r_lrange_other 10.609 r_scangle_it 10.083 r_scangle_other 10.025 r_dihedral_angle_2_deg 8.925 r_scbond_it 7.962 r_scbond_other 7.646 r_mcangle_other 7.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.607 r_dihedral_angle_3_deg 15.553 r_lrange_it 10.683 r_lrange_other 10.609 r_scangle_it 10.083 r_scangle_other 10.025 r_dihedral_angle_2_deg 8.925 r_scbond_it 7.962 r_scbond_other 7.646 r_mcangle_other 7.325 r_mcangle_it 7.322 r_dihedral_angle_1_deg 6.434 r_mcbond_it 5.641 r_mcbond_other 5.641 r_angle_refined_deg 2.747 r_angle_other_deg 0.804 r_symmetry_nbd_refined 0.279 r_nbd_refined 0.236 r_nbd_other 0.21 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.196 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.123 r_symmetry_xyhbond_nbd_refined 0.108 r_ncsr_local_group_5 0.088 r_symmetry_nbtor_other 0.087 r_ncsr_local_group_2 0.086 r_ncsr_local_group_1 0.085 r_ncsr_local_group_6 0.085 r_ncsr_local_group_3 0.082 r_ncsr_local_group_4 0.079 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10038 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 215
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing MxCuBE data collection Coot model building