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Crystal structure of PPK2 class III from Erysipelotrichaceae bacterium in complex with AppCH2p and 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 4.6 285 MPD 20%, sodium acetate 0.1 M, sodium chloride 0.2 M
Crystal Properties Matthews coefficient Solvent content 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.888 α = 90 b = 110.734 β = 90 c = 152.585 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 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 1.7 48.9 98.4 0.193 0.0533 0.998 10.76 13.7 145127 18.53
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 1.7 1.8 99.8 2.15 0.593 0.635 1.51 12.5
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 1.7 48.9 144529 7180 99.467 0.169 0.1671 0.1671 0.1969 0.197 30.49
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] -0.228 0.946 -0.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.737 r_dihedral_angle_3_deg 13.05 r_lrange_it 8.355 r_lrange_other 8.336 r_scangle_it 6.936 r_scangle_other 6.935 r_dihedral_angle_2_deg 6.688 r_dihedral_angle_1_deg 5.95 r_scbond_it 4.704 r_scbond_other 4.703
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.737 r_dihedral_angle_3_deg 13.05 r_lrange_it 8.355 r_lrange_other 8.336 r_scangle_it 6.936 r_scangle_other 6.935 r_dihedral_angle_2_deg 6.688 r_dihedral_angle_1_deg 5.95 r_scbond_it 4.704 r_scbond_other 4.703 r_mcangle_it 3.501 r_mcangle_other 3.501 r_mcbond_it 2.396 r_mcbond_other 2.393 r_angle_refined_deg 2.211 r_dihedral_angle_other_2_deg 1.161 r_angle_other_deg 0.814 r_symmetry_nbd_refined 0.34 r_nbd_other 0.214 r_nbd_refined 0.21 r_nbtor_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.174 r_symmetry_nbd_other 0.155 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.112 r_ncsr_local_group_5 0.091 r_ncsr_local_group_3 0.086 r_ncsr_local_group_4 0.086 r_ncsr_local_group_2 0.083 r_ncsr_local_group_6 0.077 r_symmetry_nbtor_other 0.073 r_ncsr_local_group_1 0.063 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9812 Nucleic Acid Atoms Solvent Atoms 1008 Heterogen Atoms 330
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing