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Structure of phosphorylated Enzyme I of the phosphoenolpyruvate:sugar phosphotransferase system
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZYM 1zym,2bg5 experimental model PDB 2BG5 1zym,2bg5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 The protein sample (10 mg/mL) was mixed with MgCl2 and PEP to bring each additive to a final concentration of 10 mM. After ~5 min, sodium oxalate was added to a final concentration of 10 mM. Drops containing 1:1 protein and reservoir solution were equilibrated against reservoir solution containing 22% w/v polyethylene glycol 6000, 2% saturated ammonium sulfate, and 100 mM Na+HEPES., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.51 50.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.487 α = 90 b = 94.084 β = 90 c = 161.007 γ = 90
Symmetry Space Group P 21 21 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 MARRESEARCH mirrors 2000-06-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.9793 APS 17-ID
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 2.7 50 99.5 0.096 5.8 36262 36262
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) 2.7 2.8 98.7 0.326 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MOLECULAR REPLACEMENT THROUGHOUT 1zym,2bg5 2.7 50 36205 36205 1798 0.208 0.208 0.204 0.2174 0.284 0.2874 random 32
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 r_angle_refined_deg 1.8 r_bond_refined_d 0.018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8874 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement CNS refinement PHASER phasing DENZO data reduction SCALEPACK data scaling