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Crystal structure of octameric form of Nucleoside diphosphate kinase from Acinetobacter baumannii at 2.2 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4S0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 HEPES: 7.5, PEG400, 0.1MgCl2
Crystal Properties Matthews coefficient Solvent content 2.53 51.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.1 α = 80.51 b = 69.93 β = 69.94 c = 71.7 γ = 89.76
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 S 6M mirror 2017-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.96600 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 66.322 89.3 0.051 8.9 1.7 56966
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 2.2 2.239 89.1 0.375 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) 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 4S0M 2.2 66.322 54227 2739 89.24 0.21502 0.21281 0.2181 0.2576 0.2585 RANDOM 43.307
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] -0.69 -0.09 0.86 -0.9 0.34 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.975 r_dihedral_angle_4_deg 19.309 r_dihedral_angle_3_deg 16.15 r_long_range_B_refined 9.664 r_long_range_B_other 9.643 r_scangle_other 6.955 r_dihedral_angle_1_deg 5.978 r_mcangle_it 5.162 r_mcangle_other 5.162 r_scbond_it 4.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.975 r_dihedral_angle_4_deg 19.309 r_dihedral_angle_3_deg 16.15 r_long_range_B_refined 9.664 r_long_range_B_other 9.643 r_scangle_other 6.955 r_dihedral_angle_1_deg 5.978 r_mcangle_it 5.162 r_mcangle_other 5.162 r_scbond_it 4.472 r_scbond_other 4.472 r_mcbond_it 3.463 r_mcbond_other 3.462 r_angle_refined_deg 1.624 r_angle_other_deg 1.014 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8704 Nucleic Acid Atoms Solvent Atoms 500 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling MOLREP phasing