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Crystal structure of a ROK family glucokinase from Streptomyces griseus in complex with glucose and AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VGM PDB ENTRY 3VGM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 0.1M Tris-HCl, 0.75M sodium citrate, 0.2M NaCl, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.86 57.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.58 α = 90 b = 87.73 β = 90 c = 125.39 γ = 90
Symmetry Space Group I 2 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 1.55 20 96 0.051 20.14 53724 -3 26
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 1.55 1.59 70.9 0.346 0.445 2.68
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 3VGM 1.55 20 53724 2715 96.03 0.1786 0.1774 0.1912 0.2024 0.2171 RANDOM 23.5184
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] 1.51 -0.75 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.536 r_dihedral_angle_4_deg 15.345 r_dihedral_angle_3_deg 13.845 r_dihedral_angle_1_deg 5.493 r_scangle_it 3.379 r_scbond_it 2.093 r_angle_refined_deg 1.308 r_mcangle_it 1.239 r_mcbond_it 0.67 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.536 r_dihedral_angle_4_deg 15.345 r_dihedral_angle_3_deg 13.845 r_dihedral_angle_1_deg 5.493 r_scangle_it 3.379 r_scbond_it 2.093 r_angle_refined_deg 1.308 r_mcangle_it 1.239 r_mcbond_it 0.67 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2271 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 41
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing