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Crystal structure of the glycogen synthase from A. tumefaciens in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RZV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 PEG 4000, isopropanol, HEPES, ADP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.5 50.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.357 α = 90 b = 88.115 β = 98.19 c = 84.463 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 110 CCD ADSC QUANTUM 210 channel - cut Si monochromator + cylindrical grazing incidence mirror 2003-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9393 ESRF ID29
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 2.3 50 90.7 0.084 0.062 6.9 1.8 40385 40385 42.18
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 2.3 2.42 85.5 0.337 0.062 2.9 1.8 5557
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 2.3 50 40371 40371 4055 90.7 0.18434 0.18434 0.17983 0.1848 0.22328 0.2305 RANDOM 22.453
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] -0.75 -0.4 1.47 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.586 r_scangle_it 3.604 r_dihedral_angle_1_deg 3.525 r_scbond_it 2.232 r_angle_refined_deg 1.804 r_mcangle_it 1.33 r_angle_other_deg 0.848 r_mcbond_it 0.741 r_symmetry_hbond_refined 0.379 r_symmetry_vdw_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.586 r_scangle_it 3.604 r_dihedral_angle_1_deg 3.525 r_scbond_it 2.232 r_angle_refined_deg 1.804 r_mcangle_it 1.33 r_angle_other_deg 0.848 r_mcbond_it 0.741 r_symmetry_hbond_refined 0.379 r_symmetry_vdw_refined 0.296 r_nbd_refined 0.242 r_nbd_other 0.227 r_symmetry_vdw_other 0.225 r_xyhbond_nbd_refined 0.161 r_xyhbond_nbd_other 0.15 r_chiral_restr 0.126 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7232 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling TRUNCATE data scaling AMoRE phasing