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Human glucokinase in complex with a synthetic activator
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 6.6 298 30 % PEG 1500, HEPES, PH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.9 57.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.732 α = 90 b = 79.732 β = 90 c = 321.975 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 DIFFRACTOMETER WEISSENBERG 2002-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6B 1.000 Photon Factory BL-6B
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 2.2 50 94.5 0.064 0.064 16.5 5 32108 30342 36.1
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) 2.2 2.28 0.254 1.86
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1V4S 2.2 42.37 28759 1529 94.66 0.2285 0.22588 0.22 0.27702 0.2698 RANDOM 35.812
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] 1.68 0.84 1.68 -2.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.394 r_dihedral_angle_4_deg 20.262 r_dihedral_angle_3_deg 19.34 r_dihedral_angle_1_deg 6.865 r_scangle_it 5.673 r_scbond_it 3.511 r_mcangle_it 2.358 r_angle_refined_deg 2.06 r_mcbond_it 1.305 r_symmetry_vdw_refined 0.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.394 r_dihedral_angle_4_deg 20.262 r_dihedral_angle_3_deg 19.34 r_dihedral_angle_1_deg 6.865 r_scangle_it 5.673 r_scbond_it 3.511 r_mcangle_it 2.358 r_angle_refined_deg 2.06 r_mcbond_it 1.305 r_symmetry_vdw_refined 0.449 r_symmetry_hbond_refined 0.369 r_nbtor_refined 0.31 r_nbd_refined 0.239 r_xyhbond_nbd_refined 0.191 r_chiral_restr 0.146 r_metal_ion_refined 0.142 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 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_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 3505 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement WEIS data scaling HKL-2000 data reduction HKL-2000 data scaling