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Glycogen phosphorylase in complex with chlorogenic acid.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JTU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.8 289 10mM BES Buffer
Crystal Properties Matthews coefficient Solvent content 2.59 52.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.95 α = 90 b = 128.95 β = 90 c = 116.72 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 CCD MAR CCD 165 mm 2015-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.043 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.95 30 100 0.101 7.7 5.73 52193
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 1.95 1.98 100 1.9
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 MOLECULAR REPLACEMENT THROUGHOUT 5JTU 1.95 30 52193 2766 76.32 0.14021 0.13821 0.1531 0.17744 0.1887 RANDOM 35.949
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] 0.42 0.42 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.795 r_dihedral_angle_4_deg 18.598 r_dihedral_angle_3_deg 13.785 r_long_range_B_refined 9.169 r_long_range_B_other 9.168 r_scangle_other 7.555 r_dihedral_angle_1_deg 6.047 r_scbond_it 5.081 r_scbond_other 5.081 r_mcangle_other 3.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.795 r_dihedral_angle_4_deg 18.598 r_dihedral_angle_3_deg 13.785 r_long_range_B_refined 9.169 r_long_range_B_other 9.168 r_scangle_other 7.555 r_dihedral_angle_1_deg 6.047 r_scbond_it 5.081 r_scbond_other 5.081 r_mcangle_other 3.836 r_mcangle_it 3.833 r_mcbond_it 2.939 r_mcbond_other 2.845 r_angle_refined_deg 1.439 r_angle_other_deg 0.978 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 6583 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling