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Ternary complex of human pancreatic glucokinase crystallized with activator, glucose and AMP-PNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V4S PDB ENTRY 1V4S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67 α = 90 b = 82.6 β = 90 c = 86.8 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 PIXEL PSI PILATUS 6M 2008-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 2.4 19.94 95.8 0.09 0.08 16.8 6.3 19433 18612 2 2
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 2.4 2.5 91.5 0.42 0.39 5.2 6.5 2015
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1V4S 2.4 19.94 18338 966 100 0.20512 0.20123 0.2131 0.27908 0.2922 RANDOM 33.177
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] 0.92 1.03 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.087 r_dihedral_angle_4_deg 19.341 r_dihedral_angle_3_deg 18.651 r_dihedral_angle_1_deg 5.864 r_scangle_it 2.698 r_scbond_it 1.625 r_angle_refined_deg 1.513 r_mcangle_it 1.158 r_mcbond_it 0.612 r_symmetry_hbond_refined 0.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.087 r_dihedral_angle_4_deg 19.341 r_dihedral_angle_3_deg 18.651 r_dihedral_angle_1_deg 5.864 r_scangle_it 2.698 r_scbond_it 1.625 r_angle_refined_deg 1.513 r_mcangle_it 1.158 r_mcbond_it 0.612 r_symmetry_hbond_refined 0.399 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.23 r_metal_ion_refined 0.203 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3535 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 68
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling