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Crystal Structure of the Adenylate Sensor from AMP-activated Protein Kinase in complex with ADP and ATP
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 ATP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.263 α = 90 b = 78.365 β = 124.18 c = 109.014 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 2.4 50 99.2 0.087 19.7 7 47233 45186 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 2.4 2.49 99.2 0.517 3.5 4.7
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2ooy 2.41 35.94 42900 2279 98.91 0.199 0.19171 0.18793 0.26155 0.2974 RANDOM 52.553
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] -2.15 -1.86 0.56 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.659 r_dihedral_angle_3_deg 20.365 r_dihedral_angle_4_deg 18.893 r_dihedral_angle_1_deg 6.94 r_scangle_it 2.962 r_scbond_it 1.93 r_angle_refined_deg 1.748 r_mcangle_it 1.236 r_mcbond_it 0.751 r_symmetry_hbond_refined 0.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.659 r_dihedral_angle_3_deg 20.365 r_dihedral_angle_4_deg 18.893 r_dihedral_angle_1_deg 6.94 r_scangle_it 2.962 r_scbond_it 1.93 r_angle_refined_deg 1.748 r_mcangle_it 1.236 r_mcbond_it 0.751 r_symmetry_hbond_refined 0.354 r_xyhbond_nbd_refined 0.328 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.23 r_chiral_restr 0.117 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 8350 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 178
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling CNS phasing