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Crystal structure of monomeric glycogen synthase from Pyrococcus abyssi
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, SITTING DROP 277 ammonium sulfate, potassium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.52 72.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.604 α = 90 b = 119.017 β = 90 c = 141.101 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 ADSC QUANTUM 210r Mirrors 2009-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.98020 ESRF BM16
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 2.6 25 85 0.056 0.095 10 4.8 45476 44800 2 2 14.7
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 2.6 2.74 83 0.45 0.1 2.8 4.7 6702
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BIS 2.6 24.91 45476 44724 2023 83.72 0.199 0.198 0.2118 0.228 0.2366 RANDOM 38.304
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] -0.57 -1.88 2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.987 r_dihedral_angle_4_deg 21.739 r_dihedral_angle_3_deg 19.991 r_scangle_it 8.155 r_scbond_it 6.423 r_dihedral_angle_1_deg 5.909 r_mcangle_it 4.122 r_mcbond_it 3.352 r_angle_refined_deg 1.57 r_angle_other_deg 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.987 r_dihedral_angle_4_deg 21.739 r_dihedral_angle_3_deg 19.991 r_scangle_it 8.155 r_scbond_it 6.423 r_dihedral_angle_1_deg 5.909 r_mcangle_it 4.122 r_mcbond_it 3.352 r_angle_refined_deg 1.57 r_angle_other_deg 1.04 r_chiral_restr 0.077 r_mcbond_other 0.038 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6788 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling MOLREP phasing