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Crystal structure of alpha-agarase AGA from Catenovulum maritimum
Serial Crystallography (SX)
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 7.8 278 Ammonium Sulfate, HEPES pH7.8, PEG8000
Crystal Properties Matthews coefficient Solvent content 2.79 55.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.242 α = 90 b = 136.065 β = 90 c = 109.173 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 278 PIXEL DECTRIS PILATUS 12M 2024-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979137 SSRF BL02U1
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.64 109.17 100 0.046 0.048 0.013 0.997 9 13.7 234458
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.76 100 0.047 0.049 0.013 10.7 13.2
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 1.64 109.17 222367 11632 99.84 0.18876 0.1871 0.1919 0.22012 0.2208 RANDOM 22.255
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] 0.64 -0.57 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.706 r_dihedral_angle_2_deg 7.798 r_dihedral_angle_1_deg 7.204 r_long_range_B_refined 6.563 r_long_range_B_other 6.447 r_scangle_other 4.706 r_mcangle_it 3.242 r_mcangle_other 3.242 r_scbond_it 3.111 r_scbond_other 3.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.706 r_dihedral_angle_2_deg 7.798 r_dihedral_angle_1_deg 7.204 r_long_range_B_refined 6.563 r_long_range_B_other 6.447 r_scangle_other 4.706 r_mcangle_it 3.242 r_mcangle_other 3.242 r_scbond_it 3.111 r_scbond_other 3.024 r_mcbond_it 2.245 r_mcbond_other 2.245 r_angle_refined_deg 1.664 r_angle_other_deg 0.594 r_chiral_restr 0.087 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 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 12198 Nucleic Acid Atoms Solvent Atoms 1367 Heterogen Atoms 162
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing