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Crystal structure of an N-terminal cyclic nucleotide-binding domain of a PycTIR from Novosphingobium pentaromativorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M ammonium acetate,
0.01 M calcium chloride dihydrate,0.05 M sodium cacodylate trihydrate pH 6.5,10% w/v polyethylene glycol 4,000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.115 α = 90 b = 87.115 β = 90 c = 93.349 γ = 120
Symmetry Space Group P 65 2 2
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 16M 2022-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 07A 0.97626 NSRRC TPS 07A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.858 30 99.8 0.998 85 34.5 5229
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.86 2.96 100 0.895 2.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT AlphaFold 2.858 24.345 4901 247 93.817 0.259 0.2578 0.2601 0.282 0.3168 53.472
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] -0.041 -0.021 -0.041 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.882 r_dihedral_angle_3_deg 22.793 r_dihedral_angle_4_deg 19.384 r_lrange_other 12.761 r_lrange_it 12.706 r_dihedral_angle_1_deg 8.969 r_scangle_it 7.749 r_scangle_other 7.743 r_mcangle_other 6.89 r_mcangle_it 6.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.882 r_dihedral_angle_3_deg 22.793 r_dihedral_angle_4_deg 19.384 r_lrange_other 12.761 r_lrange_it 12.706 r_dihedral_angle_1_deg 8.969 r_scangle_it 7.749 r_scangle_other 7.743 r_mcangle_other 6.89 r_mcangle_it 6.882 r_scbond_it 4.801 r_scbond_other 4.798 r_mcbond_it 4.218 r_mcbond_other 4.208 r_angle_refined_deg 1.451 r_angle_other_deg 1.135 r_symmetry_nbd_refined 0.282 r_nbd_other 0.246 r_nbd_refined 0.245 r_symmetry_nbd_other 0.224 r_symmetry_xyhbond_nbd_refined 0.208 r_xyhbond_nbd_refined 0.204 r_nbtor_refined 0.156 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.065 r_chiral_restr 0.047 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1017 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing