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Human glucokinase in complex with a synthetic activator
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 298K
Crystal Properties Matthews coefficient Solvent content 2.96 58.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.793 α = 90 b = 79.793 β = 90 c = 326.124 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 IMAGE PLATE RIGAKU RAXIS V mirrors 2004-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.000 SPring-8 BL32B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.11 50 94.5 0.048 31.93 5.6 34817
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) 2.11 2.19 83 0.292 2.3 2943
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT 2.11 47.46 34816 1733 94.67 0.235 0.232 0.284 0.2705 RANDOM 39.888
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] 0.25 0.13 0.25 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.942 r_dihedral_angle_4_deg 21.354 r_dihedral_angle_3_deg 19.052 r_dihedral_angle_1_deg 6.313 r_scangle_it 5.453 r_scbond_it 3.483 r_mcangle_it 2.338 r_angle_refined_deg 2.013 r_mcbond_it 1.322 r_symmetry_vdw_refined 0.443
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.942 r_dihedral_angle_4_deg 21.354 r_dihedral_angle_3_deg 19.052 r_dihedral_angle_1_deg 6.313 r_scangle_it 5.453 r_scbond_it 3.483 r_mcangle_it 2.338 r_angle_refined_deg 2.013 r_mcbond_it 1.322 r_symmetry_vdw_refined 0.443 r_nbd_other 0.441 r_xyhbond_nbd_other 0.342 r_nbtor_refined 0.31 r_metal_ion_refined 0.29 r_symmetry_hbond_refined 0.251 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.151 r_bond_refined_d 0.023 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3492 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 47
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction