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Crystal structure of the adenylate sensor from AMP-activated protein kinase in complex with ADP and AMP
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, 5mM ADP, 5mM AMP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.293 α = 90 b = 78.087 β = 124.13 c = 108.553 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 2.7 50 96.8 0.107 7.4 3.4 31934 30918 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 2.7 2.8 81.6 0.472 1.5 2.4
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 (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 2ooy 2.7 48.28 30918 29358 1558 96.31 0.2106 0.20641 0.2031 0.28945 0.2765 RANDOM 52.865
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] -1.7 -1.58 -0.57 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.552 r_dihedral_angle_3_deg 20.538 r_dihedral_angle_4_deg 18.171 r_dihedral_angle_1_deg 7.039 r_scangle_it 2.139 r_angle_refined_deg 1.609 r_scbond_it 1.322 r_mcangle_it 0.928 r_mcbond_it 0.526 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.552 r_dihedral_angle_3_deg 20.538 r_dihedral_angle_4_deg 18.171 r_dihedral_angle_1_deg 7.039 r_scangle_it 2.139 r_angle_refined_deg 1.609 r_scbond_it 1.322 r_mcangle_it 0.928 r_mcbond_it 0.526 r_nbtor_refined 0.321 r_nbd_refined 0.239 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.184 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.112 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8349 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling CNS phasing