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Crystal structure of nucleoside diphosphate kinase (NDK) from Streptococcus pneumoniae in complex with ADP and vanadate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9RVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 24% PEG 3350, 100 mM MES pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.6 65.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 198.83 α = 90 b = 198.83 β = 90 c = 72.28 γ = 90
Symmetry Space Group P 41 21 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 PILATUS3 2M 2021-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.42 72.28 99.7 0.376 0.412 0.165 0.914 4.5 5.8 20087
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.42 3.69 99.8 0.978 1.068 0.419 0.802 6.1
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 THROUGHOUT 3.42 70.396 20005 1027 99.231 0.207 0.204 0.2103 0.2688 0.2668 RANDOM 64.535
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] 2.019 2.019 -4.038
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.945 r_dihedral_angle_6_deg 13.478 r_lrange_it 11.401 r_lrange_other 11.4 r_dihedral_angle_2_deg 8.899 r_scangle_it 7.89 r_scangle_other 7.886 r_dihedral_angle_1_deg 7.593 r_mcangle_it 7.304 r_mcangle_other 7.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.945 r_dihedral_angle_6_deg 13.478 r_lrange_it 11.401 r_lrange_other 11.4 r_dihedral_angle_2_deg 8.899 r_scangle_it 7.89 r_scangle_other 7.886 r_dihedral_angle_1_deg 7.593 r_mcangle_it 7.304 r_mcangle_other 7.303 r_scbond_it 4.632 r_scbond_other 4.626 r_mcbond_it 4.385 r_mcbond_other 4.384 r_angle_refined_deg 1.448 r_angle_other_deg 0.489 r_nbd_refined 0.216 r_metal_ion_refined 0.202 r_symmetry_nbd_other 0.201 r_symmetry_nbd_refined 0.188 r_nbd_other 0.186 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.171 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.066 r_dihedral_angle_other_2_deg 0.051 r_symmetry_xyhbond_nbd_other 0.039 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 6588 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 133
Software Software Software Name Purpose iMOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction