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Crystal structure of an N-terminal cyclic nucleotide-binding domain of a PycTIR from Pseudovibrio sp. in complex with cUMP
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 0.075 M HEPES pH 7.5, 7.5% w/v polyethylene glycol 8,000, 6% v/v ethylene glycol and 25% v/v glycerol
Crystal Properties Matthews coefficient Solvent content 2.13 42.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.485 α = 90 b = 133.485 β = 90 c = 34.069 γ = 90
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 2.401 30 99.8 1 23.6 10.5 12049
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 2.41 2.5 100 0.808 2.7 11
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 2.401 25.082 11953 664 98.826 0.2 0.1979 0.2014 0.2436 0.2534 37.905
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] 0.034 0.034 -0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.703 r_dihedral_angle_3_deg 20.089 r_dihedral_angle_4_deg 17.812 r_dihedral_angle_1_deg 7.672 r_lrange_it 7.324 r_lrange_other 7.324 r_scangle_it 5.203 r_scangle_other 5.202 r_mcangle_it 4.297 r_mcangle_other 4.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.703 r_dihedral_angle_3_deg 20.089 r_dihedral_angle_4_deg 17.812 r_dihedral_angle_1_deg 7.672 r_lrange_it 7.324 r_lrange_other 7.324 r_scangle_it 5.203 r_scangle_other 5.202 r_mcangle_it 4.297 r_mcangle_other 4.297 r_scbond_it 3.194 r_scbond_other 3.193 r_mcbond_it 2.808 r_mcbond_other 2.806 r_angle_refined_deg 1.33 r_angle_other_deg 1.149 r_symmetry_xyhbond_nbd_refined 0.218 r_nbd_refined 0.201 r_symmetry_nbd_refined 0.201 r_nbd_other 0.196 r_symmetry_nbd_other 0.193 r_xyhbond_nbd_refined 0.156 r_nbtor_refined 0.145 r_symmetry_nbtor_other 0.077 r_xyhbond_nbd_other 0.077 r_chiral_restr 0.052 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2498 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing