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Crystal structure of the adenylate sensor from AMP-activated protein kinase in complex with 5-aminoimidazole-4-carboxamide 1-beta-D-ribofuranotide (ZMP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 6-10% PEG 3350, 0.1M sodium citrate, pH 5.5, 2mM ZMP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.47 α = 90 b = 78.146 β = 124.04 c = 108.512 γ = 90
Symmetry Space Group C 1 2 1
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 2007-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97926 APS 24-ID-C
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 3 50 89.3 0.18 4.6 3.9 21790 20826 1 1
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 3 3.11 96 0.63 1.5 3.3 2232
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 FOURIER SYNTHESIS THROUGHOUT 200y 3.01 41.34 1 1 20590 19774 1048 89.15 0.303 0.23853 0.2354 0.2475 0.29736 0.2685 RANDOM 89.957
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] -0.47 -1.53 -0.62 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.578 r_dihedral_angle_3_deg 21.108 r_dihedral_angle_4_deg 18.907 r_dihedral_angle_1_deg 6.465 r_scangle_it 1.466 r_angle_refined_deg 1.439 r_scbond_it 0.889 r_mcangle_it 0.657 r_mcbond_it 0.366 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.578 r_dihedral_angle_3_deg 21.108 r_dihedral_angle_4_deg 18.907 r_dihedral_angle_1_deg 6.465 r_scangle_it 1.466 r_angle_refined_deg 1.439 r_scbond_it 0.889 r_mcangle_it 0.657 r_mcbond_it 0.366 r_nbtor_refined 0.311 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.21 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8130 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling CNS phasing