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The R-state Glycogen Phosphorylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9GPB pdb entry 9gpb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 7.5 289 1.1-1.3 M ammonium sulfate, 10mM beta-glycerophosphate buffer pH 7.5, 0.5mM EDTA, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.41 48.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.895 α = 90 b = 189.92 β = 109.27 c = 88.16 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 225 mm CCD 2008-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 0.97976 SRS PX10.1
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 2.59 30 99.6 0.064 11.7 3.4 112937 107281 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 99.6 0.358 3.89 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT pdb entry 9gpb 2.59 29.59 107281 107281 5654 99.29 0.20958 0.20656 0.207 0.26577 0.2658 RANDOM 49.826
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] -1.95 -0.36 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.841 r_dihedral_angle_3_deg 21.501 r_dihedral_angle_4_deg 19.187 r_dihedral_angle_1_deg 6.261 r_scangle_it 1.889 r_angle_refined_deg 1.341 r_scbond_it 1.125 r_mcangle_it 0.851 r_mcbond_it 0.471 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.841 r_dihedral_angle_3_deg 21.501 r_dihedral_angle_4_deg 19.187 r_dihedral_angle_1_deg 6.261 r_scangle_it 1.889 r_angle_refined_deg 1.341 r_scbond_it 1.125 r_mcangle_it 0.851 r_mcbond_it 0.471 r_nbtor_refined 0.312 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.096 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26363 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling REFMAC phasing