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The crystal structure of Glycogen Phosphorylase in complex with 10h
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other native T-state of GPb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.7 289 10 mM BES buffer
Crystal Properties Matthews coefficient Solvent content 2.48 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.595 α = 90 b = 128.595 β = 90 c = 116.648 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 2017-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 91 100 0.213 9.1 14.5 50194
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 100 2.8 14.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT native T-state of GPb 2.2 90.93 47694 2438 99.98 0.14366 0.14221 0.1519 0.17224 0.177 RANDOM 43.795
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] 1.01 1.01 -2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.261 r_dihedral_angle_4_deg 18.551 r_dihedral_angle_3_deg 13.532 r_long_range_B_refined 6.623 r_long_range_B_other 6.623 r_dihedral_angle_1_deg 5.984 r_scangle_other 5.137 r_scbond_it 3.215 r_scbond_other 3.215 r_mcangle_it 3.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.261 r_dihedral_angle_4_deg 18.551 r_dihedral_angle_3_deg 13.532 r_long_range_B_refined 6.623 r_long_range_B_other 6.623 r_dihedral_angle_1_deg 5.984 r_scangle_other 5.137 r_scbond_it 3.215 r_scbond_other 3.215 r_mcangle_it 3.118 r_mcangle_other 3.118 r_mcbond_it 2.07 r_mcbond_other 2.069 r_angle_refined_deg 1.35 r_angle_other_deg 0.967 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 6589 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing