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A glucose-based molecular rotor probes the catalytic site of glycogen phosphorylase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.8 289 N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid, EDTA, DTT, IMP
Crystal Properties Matthews coefficient Solvent content 2.47 50.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.602 α = 90 b = 128.602 β = 90 c = 116.71 γ = 90
Symmetry Space Group P 43 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 293 PIXEL DECTRIS PILATUS 6M-F 2019-08-23 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 1.8 128.6 100 0.999 21.4 20.4 90796 31.5
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 1.8 1.83 0.769
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5MEM 1.8 30.002 90684 4661 99.961 0.159 0.1583 0.1593 0.1805 0.1814 38.558
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] 1.103 1.103 -2.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.657 r_dihedral_angle_4_deg 17.999 r_dihedral_angle_3_deg 13.277 r_lrange_it 6.465 r_lrange_other 6.455 r_dihedral_angle_1_deg 6.34 r_scangle_it 5.029 r_scangle_other 5.029 r_mcangle_it 3.208 r_mcangle_other 3.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.657 r_dihedral_angle_4_deg 17.999 r_dihedral_angle_3_deg 13.277 r_lrange_it 6.465 r_lrange_other 6.455 r_dihedral_angle_1_deg 6.34 r_scangle_it 5.029 r_scangle_other 5.029 r_mcangle_it 3.208 r_mcangle_other 3.207 r_scbond_it 3.143 r_scbond_other 3.142 r_mcbond_it 2.207 r_mcbond_other 2.207 r_angle_refined_deg 1.313 r_angle_other_deg 1.278 r_symmetry_xyhbond_nbd_refined 0.22 r_nbd_refined 0.197 r_symmetry_nbd_other 0.173 r_nbd_other 0.17 r_nbtor_refined 0.162 r_symmetry_nbd_refined 0.158 r_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.068 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6587 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing