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Crystal structure of a ROK family glucokinase from Streptomyces griseus
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 7.5 293 0.1M Tris-HCl (pH 7.5), 16% PEG 3350, 0.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.81 67.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.69 α = 90 b = 173.7 β = 106.69 c = 124.03 γ = 90
Symmetry Space Group P 1 21 1
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 3.25 20 96.3 0.113 10.15 60768 -3 76.659
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 3.25 3.33 97.6 0.829 0.954 2.14
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 3.25 20 60748 6121 96.85 0.2119 0.2059 0.2054 0.2644 0.2571 RANDOM 87.3443
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] -0.39 -1.54 0.87 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.942 r_dihedral_angle_3_deg 19.556 r_dihedral_angle_4_deg 17.879 r_dihedral_angle_1_deg 6.464 r_scangle_it 1.828 r_angle_refined_deg 1.449 r_scbond_it 1.008 r_angle_other_deg 0.919 r_mcangle_it 0.899 r_mcbond_it 0.469
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.942 r_dihedral_angle_3_deg 19.556 r_dihedral_angle_4_deg 17.879 r_dihedral_angle_1_deg 6.464 r_scangle_it 1.828 r_angle_refined_deg 1.449 r_scbond_it 1.008 r_angle_other_deg 0.919 r_mcangle_it 0.899 r_mcbond_it 0.469 r_mcbond_other 0.081 r_chiral_restr 0.073 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18124 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 18
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing