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Crystal structure of Nucleoside diphosphate kinase from Pseudomonas aeruginosa at 3.55 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YOL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.1M Sodium Malonate, 20% PEG 3350, PH-8.0.
Crystal Properties Matthews coefficient Solvent content 2.6 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.566 α = 99.6 b = 70.875 β = 109.12 c = 71.097 γ = 90.25
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 2018-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.953 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.55 45.98 97.5 0.2 3.8 18.6 14065
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.55 3.64 98.8 0.75 1.5
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 5YOL 3.55 45.98 14065 741 98.63 0.28852 0.28622 0.2873 0.33174 0.3298 RANDOM 70
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] 2.44 3.41 0.61 -0.93 -0.47 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.806 r_long_range_B_refined 19.594 r_long_range_B_other 19.594 r_dihedral_angle_3_deg 19.314 r_dihedral_angle_4_deg 19.269 r_mcangle_it 9.962 r_mcangle_other 9.961 r_scangle_other 9.412 r_dihedral_angle_1_deg 7.702 r_mcbond_it 5.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.806 r_long_range_B_refined 19.594 r_long_range_B_other 19.594 r_dihedral_angle_3_deg 19.314 r_dihedral_angle_4_deg 19.269 r_mcangle_it 9.962 r_mcangle_other 9.961 r_scangle_other 9.412 r_dihedral_angle_1_deg 7.702 r_mcbond_it 5.833 r_mcbond_other 5.832 r_scbond_it 5.369 r_scbond_other 5.361 r_angle_refined_deg 1.729 r_angle_other_deg 0.929 r_chiral_restr 0.063 r_bond_refined_d 0.012 r_gen_planes_other 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 8752 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling MOLREP phasing