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R-State AMP Complex Reveals Initial Steps of the Quaternary Transition of Fructose-1,6-bisphosphatase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 A54L FBPase (10mg/ml), 25mM Hepes pH7.4, 5 mM MgCl2, 5mM F16P2, 5mM AMP and a precipitant solution [Hepes (100mM, pH 7.4), PEG 3350 (14% w/v), 2-methyl-2,4-pentanediol (21% v/v), and t-butanol (5% v/v)], VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.74 α = 90 b = 166.14 β = 90 c = 78.94 γ = 90
Symmetry Space Group P 21 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 110 IMAGE PLATE RIGAKU RAXIS IV CuKalpha Osmic confocal image system 2001-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 55.38 0.053 6.7 53756 53756 18.9
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 2.07 96.7 0.272 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 1EYK 2.07 6 46422 4718 99.7 0.2181 0.218 0.215 0.26 0.2542 RANDOM 37.2
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] 10.86 -7.66 -3.2
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 2.92 c_mcangle_it 2.41 c_scbond_it 2.03 c_mcbond_it 1.46 c_angle_deg 1.2 c_improper_angle_d 0.78 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 2.92 c_mcangle_it 2.41 c_scbond_it 2.03 c_mcbond_it 1.46 c_angle_deg 1.2 c_improper_angle_d 0.78 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5028 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 80
Software Software Software Name Purpose AMoRE phasing CNS refinement