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Crystal structure of human brain glycogen phosphorylase bound to AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z8D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 290 28 % (v/v) PEG 400, 0.2 M calcium chloride, and 0.1 M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.71 54.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.04 α = 90 b = 172.04 β = 90 c = 123.59 γ = 120
Symmetry Space Group P 6 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2015-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.4 47.56 99.7 27.6 19 15352
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 1Z8D 3.4 47.56 14583 768 99.73 0.20709 0.20245 0.2032 0.2951 0.2948 RANDOM 119.289
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] 0.34 0.17 0.34 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.064 r_dihedral_angle_3_deg 20.35 r_dihedral_angle_4_deg 18.814 r_long_range_B_refined 14.847 r_long_range_B_other 14.847 r_mcangle_it 9.657 r_mcangle_other 9.656 r_scangle_other 9.587 r_mcbond_it 6.266 r_mcbond_other 6.255
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.064 r_dihedral_angle_3_deg 20.35 r_dihedral_angle_4_deg 18.814 r_long_range_B_refined 14.847 r_long_range_B_other 14.847 r_mcangle_it 9.657 r_mcangle_other 9.656 r_scangle_other 9.587 r_mcbond_it 6.266 r_mcbond_other 6.255 r_scbond_it 5.95 r_scbond_other 5.949 r_dihedral_angle_1_deg 2.788 r_angle_refined_deg 1.602 r_angle_other_deg 1.135 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 6535 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing