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Crystal Structure of an ADP-Glucose Phosphorylase from Arabidopsis thaliana with bound ADP-Glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z84 PDB Entry: 1Z84
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10 MG/ML PROTEIN, 20% PEG 2000,
0.2M SODIUM CHLORIDE, 0.10M MES-ACETATE, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.318 α = 90 b = 95.454 β = 90 c = 110.504 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 BRUKER PROTEUM-R MONTEL OPTICS 2005-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.23 47.73 100 0.1912 11.28 11.78 32389
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.23 2.25 99.9 0.6756 2.92 7.34 840
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB Entry: 1Z84 2.23 47.727 32302 1639 99.91 0.179 0.1761 0.2434 0.2242 18.776
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] 0.031 -0.031 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.761 r_dihedral_angle_4_deg 25.756 r_dihedral_angle_3_deg 14.842 r_dihedral_angle_1_deg 6.73 r_scbond_it 3.722 r_scangle_it 2.784 r_mcangle_it 2.73 r_angle_refined_deg 1.664 r_mcbond_it 1.516 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.761 r_dihedral_angle_4_deg 25.756 r_dihedral_angle_3_deg 14.842 r_dihedral_angle_1_deg 6.73 r_scbond_it 3.722 r_scangle_it 2.784 r_mcangle_it 2.73 r_angle_refined_deg 1.664 r_mcbond_it 1.516 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.287 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.188 r_metal_ion_refined 0.178 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4904 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 82
Software Software Software Name Purpose SAINT data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction