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Crystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Lysinibacillus fusiformis bound to ADP (form I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CZP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Ammonium Sulfate and MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.17 61.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.782 α = 90 b = 109.782 β = 90 c = 286.68 γ = 90
Symmetry Space Group I 41 2 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 EIGER2 X 16M Two-stage focusing X-ray optics 2020-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.88 48.39 99 0.089 0.99 16.4 8.9 20089
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 2.88 3.03 1.5
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 2.88 48.39 20089 1005 98.562 0.192 0.1895 0.1961 0.2437 0.2386 92.621
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] -0.013 -0.013 0.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.53 r_lrange_it 19.881 r_lrange_other 19.881 r_dihedral_angle_2_deg 19.361 r_scangle_it 16.711 r_scangle_other 16.598 r_dihedral_angle_6_deg 14.144 r_mcangle_other 12.865 r_mcangle_it 12.86 r_scbond_it 12.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.53 r_lrange_it 19.881 r_lrange_other 19.881 r_dihedral_angle_2_deg 19.361 r_scangle_it 16.711 r_scangle_other 16.598 r_dihedral_angle_6_deg 14.144 r_mcangle_other 12.865 r_mcangle_it 12.86 r_scbond_it 12.212 r_scbond_other 12.065 r_mcbond_it 9.747 r_mcbond_other 9.738 r_dihedral_angle_1_deg 6.268 r_angle_refined_deg 1.79 r_dihedral_angle_other_2_deg 0.592 r_angle_other_deg 0.589 r_symmetry_xyhbond_nbd_refined 0.301 r_symmetry_nbd_refined 0.26 r_nbd_refined 0.237 r_nbd_other 0.21 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.194 r_xyhbond_nbd_refined 0.153 r_ncsr_local_group_1 0.109 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.079 r_bond_refined_d 0.009 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 3341 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing