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Crystal structure of nucleoside diphosphate kinase (NDK) from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q8Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.2 M calcium chloride dihydrate, 0.1 M HEPES sodium pH 7.5 and 28% v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 2.07 40.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.878 α = 90 b = 68.878 β = 90 c = 156.407 γ = 120
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 4M 2024-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.2 34.44 98.1 0.994 13.5 10.4 44110
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 0.794
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 1.2 34.44 44110 2156 98.029 0.173 0.1724 0.1799 0.1853 0.194 12.978
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] 0.305 0.153 0.305 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.182 r_dihedral_angle_3_deg 10.629 r_dihedral_angle_2_deg 8.252 r_dihedral_angle_1_deg 6.731 r_lrange_it 5.37 r_lrange_other 5.123 r_scangle_it 4.131 r_scangle_other 4.129 r_scbond_it 2.707 r_scbond_other 2.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.182 r_dihedral_angle_3_deg 10.629 r_dihedral_angle_2_deg 8.252 r_dihedral_angle_1_deg 6.731 r_lrange_it 5.37 r_lrange_other 5.123 r_scangle_it 4.131 r_scangle_other 4.129 r_scbond_it 2.707 r_scbond_other 2.705 r_mcangle_other 2.48 r_mcangle_it 2.465 r_angle_refined_deg 2.023 r_mcbond_it 1.614 r_mcbond_other 1.593 r_angle_other_deg 0.667 r_xyhbond_nbd_refined 0.257 r_nbd_refined 0.242 r_symmetry_xyhbond_nbd_refined 0.203 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.184 r_nbd_other 0.155 r_symmetry_nbd_refined 0.113 r_chiral_restr 0.112 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1088 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing