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Catalytic complex of Human Glucokinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F9M PDB ENTRY 3F9M
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 2.22 44.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.88 α = 90 b = 82.12 β = 90 c = 86.83 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 2008-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0001 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 2.15 25 84.5 0.076 0.067 17.2 3.6 26291 22231 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 2.15 2.27 84.8 0.33 0.27 3.1 2 2741
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3F9M 2.15 20 2 2 22231 21054 1125 84.5 0.19977 0.19673 0.25529 0.239 RANDOM 19.864
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] 1.12 0.46 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.578 r_dihedral_angle_4_deg 20.122 r_dihedral_angle_3_deg 17.363 r_dihedral_angle_1_deg 5.689 r_scangle_it 2.635 r_scbond_it 1.617 r_angle_refined_deg 1.267 r_mcangle_it 1.108 r_angle_other_deg 0.923 r_mcbond_it 0.583
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.578 r_dihedral_angle_4_deg 20.122 r_dihedral_angle_3_deg 17.363 r_dihedral_angle_1_deg 5.689 r_scangle_it 2.635 r_scbond_it 1.617 r_angle_refined_deg 1.267 r_mcangle_it 1.108 r_angle_other_deg 0.923 r_mcbond_it 0.583 r_symmetry_vdw_other 0.293 r_nbd_refined 0.202 r_nbd_other 0.201 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_other 0.148 r_metal_ion_refined 0.124 r_mcbond_other 0.103 r_symmetry_vdw_refined 0.101 r_nbtor_other 0.086 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3512 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement SCALA data scaling