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Rhodobacter sp. 140A Polyphosphate kinase mutant-D114K/D210S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CZQ PDB entry 3CZQ used as the molecular replacement search model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2 M MgCl2, 0.1 M Tris-HCl pH 8.5, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.23 44.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.3 α = 104.502 b = 65.45 β = 101.044 c = 90.36 γ = 100.824
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 6M 2026-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 2.43 61.459 95.5 0.065 0.996 11.9 3.5 44219
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 2.43 2.49 95.4 0.79 0.564 1.7 3.6
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 2.43 61.459 44217 2133 95.489 0.222 0.2203 0.2255 0.2669 0.2683 57.822
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] 2.186 0.167 1.51 -0.873 -0.346 -1.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.578 r_dihedral_angle_6_deg 13.523 r_lrange_it 8.779 r_lrange_other 8.777 r_scangle_it 6.271 r_scangle_other 6.265 r_dihedral_angle_1_deg 5.248 r_mcangle_it 5.133 r_mcangle_other 5.133 r_dihedral_angle_2_deg 4.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.578 r_dihedral_angle_6_deg 13.523 r_lrange_it 8.779 r_lrange_other 8.777 r_scangle_it 6.271 r_scangle_other 6.265 r_dihedral_angle_1_deg 5.248 r_mcangle_it 5.133 r_mcangle_other 5.133 r_dihedral_angle_2_deg 4.464 r_scbond_it 3.765 r_scbond_other 3.754 r_mcbond_it 3.276 r_mcbond_other 3.273 r_angle_refined_deg 1.054 r_angle_other_deg 0.389 r_symmetry_xyhbond_nbd_refined 0.274 r_symmetry_nbd_refined 0.27 r_nbd_other 0.247 r_nbd_refined 0.205 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.141 r_ncsr_local_group_3 0.084 r_ncsr_local_group_5 0.084 r_ncsr_local_group_4 0.077 r_ncsr_local_group_6 0.076 r_ncsr_local_group_1 0.075 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_other 0.071 r_ncsr_local_group_2 0.069 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9326 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing