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Crystal structure of human brain glycogen phosphorylase
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 2.69 54.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.66 α = 90 b = 171.66 β = 90 c = 122.92 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 PIXEL DECTRIS PILATUS3 6M 2015-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.980110 SOLEIL PROXIMA 1
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 2.5 47.37 99.2 20.3 26 37317
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 2.5 47.37 35450 1866 99.23 0.18916 0.18651 0.1872 0.23855 0.2315 RANDOM 69.33
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] 0.6 0.3 0.6 -1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.371 r_dihedral_angle_3_deg 18.259 r_dihedral_angle_4_deg 17.525 r_long_range_B_other 11.362 r_long_range_B_refined 11.361 r_scangle_other 8.687 r_mcangle_it 7.053 r_mcangle_other 7.053 r_scbond_it 6.093 r_scbond_other 6.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.371 r_dihedral_angle_3_deg 18.259 r_dihedral_angle_4_deg 17.525 r_long_range_B_other 11.362 r_long_range_B_refined 11.361 r_scangle_other 8.687 r_mcangle_it 7.053 r_mcangle_other 7.053 r_scbond_it 6.093 r_scbond_other 6.092 r_mcbond_it 5.165 r_mcbond_other 5.164 r_dihedral_angle_1_deg 4.569 r_angle_refined_deg 1.687 r_angle_other_deg 1.087 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 6540 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing