☰ Navigation Tabs
Crystal structure of Pyrococcus abyssi glycogen synthase with open and closed conformations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BIS PDB ENTRY 2BIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 26-30% MPD, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.83 56.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.998 α = 90 b = 139.913 β = 90 c = 159.414 γ = 90
Symmetry Space Group P 21 21 21
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 2008-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
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 2.5 25 99.7 0.078 0.099 8.4 3.9 58723 58364 2 2 55.5
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 2.5 2.64 97.6 0.41 0.32 1.1 3.7 1964
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 (All) 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 THROUGHOUT PDB ENTRY 2BIS 2.5 24.91 2 58527 58364 2950 99.39 0.288 0.216 0.214 0.2182 0.255 0.2564 RANDOM 43.416
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] -0.26 0.92 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.785 r_dihedral_angle_3_deg 14.931 r_dihedral_angle_4_deg 13.818 r_dihedral_angle_1_deg 4.803 r_angle_refined_deg 0.825 r_angle_other_deg 0.74 r_scangle_it 0.494 r_scbond_it 0.322 r_mcangle_it 0.245 r_mcbond_it 0.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.785 r_dihedral_angle_3_deg 14.931 r_dihedral_angle_4_deg 13.818 r_dihedral_angle_1_deg 4.803 r_angle_refined_deg 0.825 r_angle_other_deg 0.74 r_scangle_it 0.494 r_scbond_it 0.322 r_mcangle_it 0.245 r_mcbond_it 0.223 r_nbtor_refined 0.173 r_nbd_other 0.168 r_nbd_refined 0.166 r_symmetry_vdw_other 0.124 r_symmetry_vdw_refined 0.113 r_symmetry_hbond_refined 0.101 r_xyhbond_nbd_refined 0.097 r_nbtor_other 0.08 r_chiral_restr 0.05 r_mcbond_other 0.021 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10452 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling MOLREP phasing