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Structure of rabbit muscle glycogen phosphorylase in complex with ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other In house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.7 289 1.1mM IMP, 1.1mM Spermine, 0mM BES, 2.9mM DTT, 0.1mM EDTA, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.51 50.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.128 α = 90 b = 128.128 β = 90 c = 116.346 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 100 CCD ADSC QUANTUM 4 Rh coated Si mirror 2001-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.87 SRS PX9.6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.6 48.8 74.5 0.059 0.045 12 3.3 98023 94754 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 74.5 0.466 0.637 1.5 1.4 3556
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 In house model 1.6 48.8 1 127198 86732 4629 71.82 0.1889 0.1869 0.2017 0.22616 0.2283 RANDOM 16.45
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] 0.79 0.79 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.628 r_dihedral_angle_4_deg 16.728 r_dihedral_angle_3_deg 13.395 r_dihedral_angle_1_deg 5.655 r_scangle_it 1.779 r_angle_other_deg 1.324 r_scbond_it 1.241 r_angle_refined_deg 1.184 r_mcangle_it 0.756 r_mcbond_it 0.692
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.628 r_dihedral_angle_4_deg 16.728 r_dihedral_angle_3_deg 13.395 r_dihedral_angle_1_deg 5.655 r_scangle_it 1.779 r_angle_other_deg 1.324 r_scbond_it 1.241 r_angle_refined_deg 1.184 r_mcangle_it 0.756 r_mcbond_it 0.692 r_symmetry_vdw_other 0.243 r_nbd_refined 0.206 r_nbtor_refined 0.172 r_nbd_other 0.167 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.151 r_symmetry_hbond_refined 0.114 r_mcbond_other 0.103 r_symmetry_vdw_refined 0.083 r_nbtor_other 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6532 Nucleic Acid Atoms Solvent Atoms 747 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction AMoRE phasing