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Crystal structure of a uridylate cyclase from Anabaena sp.
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 0.1 M BIS-TRIS pH 6.5, 0.2 M Magnesium chloride hexahydrate, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.25 45.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.661 α = 71.21 b = 50.792 β = 83.96 c = 71.391 γ = 62.07
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 1.83 30 97.6 0.998 27.5 5.5 47377
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 1.84 1.91 95.1 0.972 5.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT AlphaFold 1.83 25.05 25040 22277 96.57 0.17765 0.17651 0.17893 0.1941 RANDOM 21.504
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] -0.08 0.16 0.09 -0.24 -0.26 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.829 r_dihedral_angle_4_deg 19.667 r_dihedral_angle_3_deg 13.744 r_long_range_B_other 8.982 r_long_range_B_refined 8.962 r_scangle_other 8.101 r_scbond_it 6.351 r_scbond_other 6.349 r_dihedral_angle_1_deg 6.171 r_mcangle_it 5.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.829 r_dihedral_angle_4_deg 19.667 r_dihedral_angle_3_deg 13.744 r_long_range_B_other 8.982 r_long_range_B_refined 8.962 r_scangle_other 8.101 r_scbond_it 6.351 r_scbond_other 6.349 r_dihedral_angle_1_deg 6.171 r_mcangle_it 5.986 r_mcangle_other 5.986 r_mcbond_it 4.749 r_mcbond_other 4.699 r_angle_other_deg 2.225 r_angle_refined_deg 1.731 r_chiral_restr 0.097 r_bond_other_d 0.034 r_bond_refined_d 0.014 r_gen_planes_other 0.005 r_gen_planes_refined 0.004 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 4168 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing