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Human pancreatic glucokinase in complex with glucose and activator showing a mobile flap
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 2.15 42.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.7 α = 90 b = 81.2 β = 90 c = 85.6 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 2008-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 19.74 93.9 18.9 3.25 73934 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.6 85.4 3.7 3.2
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 1.5 19.74 73275 3664 100 0.19133 0.18969 0.2274 0.22213 0.2482 RANDOM 18.162
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] 0.18 0.37 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.658 r_dihedral_angle_4_deg 18.816 r_dihedral_angle_3_deg 13.964 r_dihedral_angle_1_deg 5.157 r_scangle_it 3.465 r_scbond_it 2.179 r_mcangle_it 1.393 r_angle_refined_deg 1.388 r_mcbond_it 0.873 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.658 r_dihedral_angle_4_deg 18.816 r_dihedral_angle_3_deg 13.964 r_dihedral_angle_1_deg 5.157 r_scangle_it 3.465 r_scbond_it 2.179 r_mcangle_it 1.393 r_angle_refined_deg 1.388 r_mcbond_it 0.873 r_nbtor_refined 0.314 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.136 r_symmetry_hbond_refined 0.119 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3549 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement