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Human Glucokinase in complex with a nanomolar 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 7.5 293 30% PEG 4000, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.3 α = 90 b = 81.3 β = 90 c = 85.5 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) 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 1.7 19.74 100 50333 47815 2 3
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 1.7 1.79 88.6 0.77 0.77 1.5 2.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1V4S 1.7 19.74 3 2 50333 47815 2517 100 0.19125 0.18959 0.2053 0.2226 0.2368 RANDOM 24.436
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] 0.8 0.18 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.509 r_dihedral_angle_4_deg 19.841 r_dihedral_angle_3_deg 15.862 r_dihedral_angle_1_deg 5.5 r_scangle_it 3.618 r_scbond_it 2.228 r_angle_refined_deg 1.787 r_mcangle_it 1.445 r_mcbond_it 0.899 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.509 r_dihedral_angle_4_deg 19.841 r_dihedral_angle_3_deg 15.862 r_dihedral_angle_1_deg 5.5 r_scangle_it 3.618 r_scbond_it 2.228 r_angle_refined_deg 1.787 r_mcangle_it 1.445 r_mcbond_it 0.899 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.233 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.152 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3502 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data collection MOSFLM data reduction SCALA data scaling CNS phasing