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Crystal structure of putative fructose transport system kinase (YP_612366.1) from Silicibacter sp. TM1040 at 1.95 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 NANODROP, 23.1% PEG 3350, 0.214M Sodium fluoride, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.58 52.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.28 α = 90 b = 102.28 β = 90 c = 116.63 γ = 120
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 2008-01-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97978, 0.91837, 0.97964 SSRL BL9-2
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 1.95 35.267 91.6 0.055 19.95 15859 -3 24.87
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 1.95 2.02 99.9 0.263 7.2
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 1.95 35.267 15859 792 91.63 0.167 0.165 0.1691 0.218 0.2173 RANDOM 19.647
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] -0.15 -0.07 -0.15 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.374 r_dihedral_angle_4_deg 17.496 r_dihedral_angle_3_deg 15.361 r_scangle_it 6.9 r_dihedral_angle_1_deg 5.398 r_scbond_it 4.616 r_mcangle_it 2.979 r_mcbond_it 1.808 r_angle_other_deg 1.582 r_angle_refined_deg 1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.374 r_dihedral_angle_4_deg 17.496 r_dihedral_angle_3_deg 15.361 r_scangle_it 6.9 r_dihedral_angle_1_deg 5.398 r_scbond_it 4.616 r_mcangle_it 2.979 r_mcbond_it 1.808 r_angle_other_deg 1.582 r_angle_refined_deg 1.41 r_mcbond_other 0.502 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1571 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms
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