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Crystal Structure of the Peptide-binding Protein NikA from Streptococcus agalactiae in Complex with Zinc, L-Histidine, Imidazole and Ethylene Glycol.
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 7.5 292 Protein: 12.9 mg/ml, 10mM HEPES (pH 7.2), 1mM TCEP, 2% Glycerol, 5mM Imidazole;
Screen: Classics II (D8), 0.1M HEPES (pH 7.5), 25% (w/v) PEG 3350;
Cryo: Reservoir.
Crystal Properties Matthews coefficient Solvent content 2.27 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.031 α = 90 b = 58.31 β = 107.33 c = 122.115 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) 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 1.95 30 95.4 0.106 0.106 0.131 0.076 0.986 8.7 2.5 70920 -3 23.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 94.1 0.574 0.574 0.721 0.432 0.628 1.6 2.4
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 29.16 67219 3668 92.55 0.18962 0.18688 0.1997 0.23918 0.2502 RANDOM 28.466
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] 3.26 4.44 -9.04 5.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 5.987 r_long_range_B_refined 4.939 r_long_range_B_other 4.895 r_dihedral_angle_1_deg 2.767 r_scangle_other 2.753 r_mcangle_it 1.96 r_mcangle_other 1.96 r_scbond_it 1.721 r_scbond_other 1.72 r_dihedral_angle_2_deg 1.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 5.987 r_long_range_B_refined 4.939 r_long_range_B_other 4.895 r_dihedral_angle_1_deg 2.767 r_scangle_other 2.753 r_mcangle_it 1.96 r_mcangle_other 1.96 r_scbond_it 1.721 r_scbond_other 1.72 r_dihedral_angle_2_deg 1.527 r_angle_refined_deg 1.523 r_mcbond_it 1.262 r_mcbond_other 1.262 r_angle_other_deg 0.515 r_chiral_restr 0.083 r_gen_planes_refined 0.015 r_gen_planes_other 0.012 r_bond_refined_d 0.004 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 8147 Nucleic Acid Atoms Solvent Atoms 605 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing