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Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KHT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.6 293 0.2 M Ammonium sulfate, 0.1 M HEPES pH 7.6, 25% (w/v) Polyethylene glycol monomethyl ether 2000, 5 mM adenosine 5'-triphosphate, 5 mM magnesium ions
Crystal Properties Matthews coefficient Solvent content 3.32 62.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.44 α = 90 b = 193.44 β = 90 c = 193.44 γ = 90
Symmetry Space Group F 4 3 2
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 MARMOSAIC 225 mm CCD 2007-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0 SPring-8 BL26B2
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 50 96.9 0.068 79.6 37.8 20843
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 2.07 80.5 0.306 11.4 25.2
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 MOLECULAR REPLACEMENT THROUGHOUT 1KHT 2 32.7 19709 1062 96.7 0.1612 0.1596 0.1719 0.1918 0.2056 RANDOM 24.776
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.93 r_dihedral_angle_4_deg 15.122 r_dihedral_angle_3_deg 14.22 r_dihedral_angle_1_deg 5.917 r_mcangle_it 2.958 r_angle_other_deg 2.286 r_mcbond_it 2.201 r_mcbond_other 2.199 r_angle_refined_deg 1.959 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.93 r_dihedral_angle_4_deg 15.122 r_dihedral_angle_3_deg 14.22 r_dihedral_angle_1_deg 5.917 r_mcangle_it 2.958 r_angle_other_deg 2.286 r_mcbond_it 2.201 r_mcbond_other 2.199 r_angle_refined_deg 1.959 r_chiral_restr 0.099 r_bond_other_d 0.034 r_bond_refined_d 0.015 r_gen_planes_other 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1543 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing