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Crystal structure of fructokinase (NP_810670.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.80 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 277 NANODROP, 0.2M NH4NO3, 20.0% PEG 3350, No Buffer pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.38 48.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.3 α = 90 b = 152.54 β = 90 c = 50.97 γ = 90
Symmetry Space Group C 2 2 21
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 mirror (vertical focusing) 2007-06-21 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97932 SSRL BL11-1
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 1.8 29.336 98.2 0.045 11.38 29514 -3 29.228
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) 1 1.8 1.86 87.4 0.361 2
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 1.8 29.336 29500 1494 99.03 0.174 0.172 0.1762 0.215 0.2134 RANDOM 19.001
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] 0.94 -0.73 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.14 r_dihedral_angle_4_deg 17.967 r_dihedral_angle_3_deg 13.7 r_dihedral_angle_1_deg 8.715 r_scangle_it 6.831 r_scbond_it 4.947 r_mcangle_it 2.807 r_mcbond_it 2.044 r_angle_refined_deg 1.575 r_angle_other_deg 1.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.14 r_dihedral_angle_4_deg 17.967 r_dihedral_angle_3_deg 13.7 r_dihedral_angle_1_deg 8.715 r_scangle_it 6.831 r_scbond_it 4.947 r_mcangle_it 2.807 r_mcbond_it 2.044 r_angle_refined_deg 1.575 r_angle_other_deg 1.022 r_mcbond_other 0.517 r_symmetry_vdw_other 0.295 r_symmetry_hbond_refined 0.267 r_nbd_refined 0.223 r_nbd_other 0.192 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.147 r_symmetry_vdw_refined 0.146 r_chiral_restr 0.1 r_nbtor_other 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2232 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing