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Plastidial phosphorylase Pho1 trimer from Solanum tuberosum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8R48
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.1 M Tris-HCl, 20 % w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.91 57.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 218.058 α = 90 b = 134.907 β = 91.3 c = 123.105 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS 6M 2023-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
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 3.3 123.07 97.9 0.997 9.5 3 52489
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 3.3 3.4 0.805
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 3.3 123.07 49944 2539 97.67 0.25653 0.25439 0.2535 0.30038 0.299 RANDOM 36.21
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] -8.25 2.7 11.35 -3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.942 r_dihedral_angle_4_deg 19.019 r_dihedral_angle_3_deg 18.471 r_dihedral_angle_1_deg 7.17 r_angle_refined_deg 1.268 r_chiral_restr 0.09 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.942 r_dihedral_angle_4_deg 19.019 r_dihedral_angle_3_deg 18.471 r_dihedral_angle_1_deg 7.17 r_angle_refined_deg 1.268 r_chiral_restr 0.09 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19920 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing