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Crystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Bacillus cereus Apo-form
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 8.5 295 PEG 2000 or 4000 , Tris buffer pH 8.5 and Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.92 57.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.134 α = 90 b = 116.815 β = 90 c = 130.54 γ = 90
Symmetry Space Group I 2 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 EIGER 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 2.42 48.604 98.6 0.11 0.99 8.6 6.4 26950
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.42 2.52 1.07 0.53
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.55 48.604 23540 1177 99.733 0.213 0.21 0.217 0.273 0.2718 RANDOM 62.603
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] 0.008 -0.035 0.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.311 r_dihedral_angle_6_deg 15.048 r_lrange_other 12.896 r_lrange_it 12.893 r_scangle_it 10.716 r_scangle_other 10.66 r_dihedral_angle_2_deg 9.141 r_mcangle_it 8.62 r_mcangle_other 8.619 r_scbond_it 7.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.311 r_dihedral_angle_6_deg 15.048 r_lrange_other 12.896 r_lrange_it 12.893 r_scangle_it 10.716 r_scangle_other 10.66 r_dihedral_angle_2_deg 9.141 r_mcangle_it 8.62 r_mcangle_other 8.619 r_scbond_it 7.249 r_scbond_other 7.156 r_dihedral_angle_1_deg 6.752 r_mcbond_it 6.068 r_mcbond_other 6.068 r_angle_refined_deg 1.678 r_angle_other_deg 0.587 r_nbd_refined 0.226 r_symmetry_nbd_other 0.195 r_symmetry_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.148 r_symmetry_nbd_refined 0.144 r_nbd_other 0.131 r_ncsr_local_group_1 0.112 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.007 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 4288 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction AutoProcess data processing Coot model building PHASER phasing