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Crystal structure of Glucokinase (BDI_1628) from Parabacteroides distasonis ATCC 8503 at 3.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 277 10.0000% Glycerol, 3.6000M NaFormate, No Buffer pH 7.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.96 58.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.732 α = 90 b = 80.732 β = 90 c = 142.581 γ = 90
Symmetry Space Group P 43 21 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 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-07-30 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97911 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 28.748 99.9 0.13 0.13 14.8 7 10015 70.492
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) 3 3.08 100 0.716 0.716 1.1 7.3 714
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 3 28.748 9970 477 99.81 0.209 0.206 0.2018 0.249 0.2339 RANDOM 53.803
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] -1.8 -1.8 3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.812 r_dihedral_angle_3_deg 13.335 r_dihedral_angle_4_deg 11.117 r_scangle_it 4.437 r_dihedral_angle_1_deg 3.396 r_scbond_it 2.578 r_mcangle_it 1.722 r_angle_refined_deg 0.919 r_mcbond_it 0.839 r_angle_other_deg 0.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.812 r_dihedral_angle_3_deg 13.335 r_dihedral_angle_4_deg 11.117 r_scangle_it 4.437 r_dihedral_angle_1_deg 3.396 r_scbond_it 2.578 r_mcangle_it 1.722 r_angle_refined_deg 0.919 r_mcbond_it 0.839 r_angle_other_deg 0.682 r_mcbond_other 0.064 r_chiral_restr 0.06 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2590 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing