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Crystal structure of the adenylate sensor from AMP-activated protein kinase complexed with AMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 6.2-7.2% PEG6000, 10% Ethylene glycol, 0.1M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.456 α = 90 b = 97.392 β = 90 c = 168.884 γ = 90
Symmetry Space Group P 21 21 21
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 2006-06-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97898, 0.97919 NSLS X4A
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 2.6 50 99.7 0.098 20.1 11.8 38169 38081 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 2.6 2.7 100 0.469
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 2.6 50 36178 1903 99.81 0.22008 0.20975 0.20627 0.2003 0.27348 0.2637 RANDOM 34.309
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] -0.94 2.22 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.383 r_dihedral_angle_3_deg 20.98 r_dihedral_angle_4_deg 18.364 r_dihedral_angle_1_deg 8.084 r_scangle_it 3.486 r_scbond_it 2.148 r_angle_refined_deg 1.804 r_mcangle_it 1.782 r_mcbond_it 1.019 r_symmetry_hbond_refined 0.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.383 r_dihedral_angle_3_deg 20.98 r_dihedral_angle_4_deg 18.364 r_dihedral_angle_1_deg 8.084 r_scangle_it 3.486 r_scbond_it 2.148 r_angle_refined_deg 1.804 r_mcangle_it 1.782 r_mcbond_it 1.019 r_symmetry_hbond_refined 0.329 r_nbtor_refined 0.321 r_xyhbond_nbd_refined 0.302 r_symmetry_vdw_refined 0.291 r_nbd_refined 0.272 r_chiral_restr 0.125 r_bond_refined_d 0.015 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 8624 Nucleic Acid Atoms Solvent Atoms 652 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling SHELXS phasing