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1.8 Angstrom Resolution Crystal Structure of cAMP-Regulatory Protein from Yersinia pestis in Complex with cAMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RYP PDB entry 3RYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 6.6 mg/mL protein, 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3, 1 mM cAMP against PACT (H12) (0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 8.5, 20% w/v PEG3350)
Crystal Properties Matthews coefficient Solvent content 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.876 α = 90 b = 82.8 β = 90 c = 106.35 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 C(111) 2018-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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) 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 1.8 30 99.1 0.058 0.058 0.062 0.021 30.5 8.5 44393 -3 29.9
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 1.8 1.83 97.3 0.722 0.722 0.776 0.278 0.874 2.9 7.5
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 PDB entry 3RYP 1.8 29.61 42181 2168 99.03 0.1761 0.17481 0.1851 0.20304 0.2162 RANDOM 41.444
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] -2.31 3.41 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.591 r_dihedral_angle_4_deg 15.577 r_dihedral_angle_3_deg 10.502 r_long_range_B_refined 6.792 r_long_range_B_other 6.698 r_scangle_other 4.51 r_dihedral_angle_1_deg 3.986 r_mcangle_it 2.928 r_mcangle_other 2.928 r_scbond_it 2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.591 r_dihedral_angle_4_deg 15.577 r_dihedral_angle_3_deg 10.502 r_long_range_B_refined 6.792 r_long_range_B_other 6.698 r_scangle_other 4.51 r_dihedral_angle_1_deg 3.986 r_mcangle_it 2.928 r_mcangle_other 2.928 r_scbond_it 2.83 r_scbond_other 2.829 r_mcbond_other 1.873 r_mcbond_it 1.872 r_angle_refined_deg 1.334 r_angle_other_deg 0.439 r_chiral_restr 0.068 r_gen_planes_refined 0.043 r_gen_planes_other 0.04 r_bond_refined_d 0.008 r_bond_other_d 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 3181 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing