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Crystal structure of putative fructosamine-3-kinase (YP_290396.1) from THERMOBIFIDA FUSCA YX-ER1 at 1.85 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 277 1.0000M LiCl, 10.0000% PEG-6000, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.68 54.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.178 α = 90 b = 91.178 β = 90 c = 82.049 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 ADSC QUANTUM 315 1m long Rh coated bent cylindrical mirror forhorizontal and vertical focussing 2008-03-23 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL1-5 0.918381,0.979224,0.978618 SSRL BL1-5
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 1.85 28.916 99.9 0.067 0.067 7.325 7 30125 28.539
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) 1 1.85 1.9 100 0.683 0.683 1.1 7.2 2199
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 1.85 28.916 30072 1522 99.81 0.167 0.165 0.1695 0.204 0.2044 RANDOM 32.77
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] 0.67 0.67 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.254 r_dihedral_angle_4_deg 17.529 r_dihedral_angle_3_deg 12.337 r_dihedral_angle_1_deg 6.49 r_scangle_it 5.706 r_scbond_it 4.246 r_mcangle_it 2.572 r_mcbond_it 1.83 r_angle_refined_deg 1.411 r_angle_other_deg 0.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.254 r_dihedral_angle_4_deg 17.529 r_dihedral_angle_3_deg 12.337 r_dihedral_angle_1_deg 6.49 r_scangle_it 5.706 r_scbond_it 4.246 r_mcangle_it 2.572 r_mcbond_it 1.83 r_angle_refined_deg 1.411 r_angle_other_deg 0.957 r_mcbond_other 0.447 r_nbd_refined 0.217 r_symmetry_vdw_other 0.209 r_nbd_other 0.202 r_symmetry_hbond_refined 0.2 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.147 r_nbtor_other 0.085 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2230 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 35
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