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Structure of butyrate kinase 2 reveals both open- and citrate-induced closed conformations: implications for substrate-induced fit conformational changes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SAZ PDB entry 1SAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 310 CRYSTALLIZATION CONDITIONS: THE PROTEIN SOLUTION CONTAINS 22.5-25 mg/ml BUK2, 25 mM TRIS-HCl pH 8.5, 400 mM NACl, 5 mM DTT, 10%(w/v) GLYCEROL. THE RESERVOIR SOLUTION IS 1ml of 77 mM PHOSPHATE-CITRATE AND 55% (w/v) PEG 200, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 310K
Crystal Properties Matthews coefficient Solvent content 3.6 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.68 α = 90 b = 193.68 β = 90 c = 122.932 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2002-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 0.9793 APS 14-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3 100 97 0.093 11.9 14.2 88518 88350 68.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 80.3 0.359 4.2 5.6 7233
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 1SAZ 3 91.48 2 88518 88350 8832 97 0.261 0.2599 0.284 0.2824 RANDOM 55.2
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.5 c_scangle_it 2.61 c_mcangle_it 2.41 c_scbond_it 1.6 c_mcbond_it 1.35 c_angle_deg 1 c_improper_angle_d 0.68 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23460 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 108
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement