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Crystal structure of a ROK family glucokinase from Streptomyces griseus in complex with glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AA4 PDB ENTRY 2AA4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.1 293 0.9M K/Na tartrate, 0.2M NaCl, 0.1M imidazole , pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.57 65.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.19 α = 90 b = 108.19 β = 90 c = 141.18 γ = 120
Symmetry Space Group P 64 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 95 CCD ADSC QUANTUM 270 2008-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.00000 Photon Factory BL-17A
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 1.84 20 99.8 0.041 32.89 42812 -3 31.781
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.89 98.9 0.33 0.365 4.31
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 2AA4 1.84 20 42812 2159 99.76 0.1683 0.1674 0.1714 0.185 0.1891 RANDOM 26.4135
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] 0.86 0.43 0.86 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.968 r_dihedral_angle_4_deg 14.953 r_dihedral_angle_3_deg 12.587 r_dihedral_angle_1_deg 5.169 r_scangle_it 4.439 r_scbond_it 2.678 r_mcangle_it 1.599 r_angle_refined_deg 1.286 r_mcbond_it 0.825 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.968 r_dihedral_angle_4_deg 14.953 r_dihedral_angle_3_deg 12.587 r_dihedral_angle_1_deg 5.169 r_scangle_it 4.439 r_scbond_it 2.678 r_mcangle_it 1.599 r_angle_refined_deg 1.286 r_mcbond_it 0.825 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2271 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 14
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing