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Crystal Structure of the Peptide-binding Protein NikA from Streptococcus agalactiae in Complex with Zinc and L-Histidine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D7R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 292 Protein: 12.9 mg/ml, 10mM HEPES (pH 7.2), 1mM TCEP, 2% Glycerol, 5mM Imidazole;
Screen: PEGs II (F8), 0.1M Sodium acetate, 25% (w/v) PEG 4000, 8% (w/v) Isopropanol;
Cryo: Reservoir.
Crystal Properties Matthews coefficient Solvent content 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.407 α = 90 b = 58.256 β = 107.95 c = 121.23 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 X 9M 2024-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92020 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.95 30 99.8 0.2 0.2 0.089 0.984 8.8 5.8 72403 -3 17.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 99.5 0.86 0.86 0.384 0.428 2.1 5.6
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 (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 1.95 29.13 68623 3760 99.06 0.17424 0.17258 0.1838 0.20348 0.2222 RANDOM 21.565
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] 0.61 0.33 -19.85 19.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 5.735 r_long_range_B_refined 3.996 r_long_range_B_other 3.892 r_dihedral_angle_1_deg 2.624 r_scangle_other 1.669 r_dihedral_angle_2_deg 1.656 r_angle_refined_deg 1.463 r_mcangle_it 1.278 r_mcangle_other 1.278 r_scbond_it 1.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 5.735 r_long_range_B_refined 3.996 r_long_range_B_other 3.892 r_dihedral_angle_1_deg 2.624 r_scangle_other 1.669 r_dihedral_angle_2_deg 1.656 r_angle_refined_deg 1.463 r_mcangle_it 1.278 r_mcangle_other 1.278 r_scbond_it 1.037 r_scbond_other 1.037 r_mcbond_it 0.756 r_mcbond_other 0.756 r_angle_other_deg 0.507 r_chiral_restr 0.082 r_gen_planes_refined 0.013 r_gen_planes_other 0.01 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 8116 Nucleic Acid Atoms Solvent Atoms 604 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing