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Plastidial phosphorylase Pho1 from Solanum tuberosum in complex with beta cyclodextrin
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 % PEG4000
Crystal Properties Matthews coefficient Solvent content 2.96 58.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 218.63 α = 90 b = 136.728 β = 91.47 c = 123.155 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 2023-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976256 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.8 123.114 98 0.09 0.995 7.4 3 87204
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.85 0.818 0.654
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.8 123.114 87192 4411 97.836 0.219 0.2176 0.2264 0.239 0.2422 RANDOM 88.194
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] -2.278 1.78 6.759 -4.566
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.186 r_dihedral_angle_6_deg 13.361 r_lrange_it 7.763 r_lrange_other 7.763 r_dihedral_angle_1_deg 6.518 r_dihedral_angle_2_deg 5.871 r_mcangle_it 3.858 r_mcangle_other 3.858 r_scangle_it 3.662 r_scangle_other 3.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.186 r_dihedral_angle_6_deg 13.361 r_lrange_it 7.763 r_lrange_other 7.763 r_dihedral_angle_1_deg 6.518 r_dihedral_angle_2_deg 5.871 r_mcangle_it 3.858 r_mcangle_other 3.858 r_scangle_it 3.662 r_scangle_other 3.662 r_mcbond_it 2.324 r_mcbond_other 2.324 r_scbond_it 2.098 r_scbond_other 2.098 r_angle_refined_deg 1.077 r_angle_other_deg 0.402 r_nbd_refined 0.222 r_symmetry_nbd_other 0.196 r_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.18 r_nbd_other 0.143 r_symmetry_nbd_refined 0.106 r_ncsr_local_group_3 0.102 r_ncsr_local_group_2 0.101 r_symmetry_xyhbond_nbd_refined 0.093 r_chiral_restr 0.092 r_ncsr_local_group_1 0.088 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20010 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 263
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing