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Crystal structure of the adenylate sensor from AMP-activated protein kinase in complex with ADP
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, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 47.07
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 2006-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 99.2 0.14 0.134 12 5.8 32417 1 2
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 2.77 68.4 0.257 3.15 2.6
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 FOURIER SYNTHESIS THROUGHOUT 2ooy 2.7 48.28 28869 1558 96.31 0.2106 0.20641 0.2294 0.28945 0.2357 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 108
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling CNS phasing