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Carbohydrate-bound structure of alpha-glucan phosphorylase from Crocosphaera subtropica ATCC 51142
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-B1WXW6-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 45% (w/v) PEG 400, 0.1M Tris-HCl pH 8.0, 0.2M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3.65 66.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 267.238 α = 90 b = 267.238 β = 90 c = 204.452 γ = 120
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 PILATUS3 6M 2023-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 2.7 93.5 100 0.074 0.083 0.038 0.799 8.2 4.9 149465
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 100 0.36 0.406 0.187 0.762 2.1 4.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 50.005 76445 3786 99.959 0.176 0.1738 0.1799 0.2267 0.2282 49.587
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] 0.008 0.004 0.008 -0.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.574 r_dihedral_angle_4_deg 18.847 r_dihedral_angle_3_deg 18.306 r_lrange_other 7.796 r_lrange_it 7.795 r_dihedral_angle_1_deg 7.125 r_scangle_it 6.356 r_scangle_other 6.356 r_mcangle_it 5.374 r_mcangle_other 5.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.574 r_dihedral_angle_4_deg 18.847 r_dihedral_angle_3_deg 18.306 r_lrange_other 7.796 r_lrange_it 7.795 r_dihedral_angle_1_deg 7.125 r_scangle_it 6.356 r_scangle_other 6.356 r_mcangle_it 5.374 r_mcangle_other 5.374 r_scbond_it 4.333 r_scbond_other 4.332 r_mcbond_it 3.765 r_mcbond_other 3.765 r_angle_refined_deg 1.667 r_angle_other_deg 1.268 r_nbd_other 0.207 r_nbd_refined 0.206 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.162 r_xyhbond_nbd_refined 0.155 r_symmetry_nbd_refined 0.153 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13172 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 328
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing