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Structure of Apo Adenylate Kinase from Aquifex Aeolicus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 298 28-30% (w/v) PEG 3000, 200 mM sodium acetate, and 100 mM TRIS, pH 8.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.55 51.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.681 α = 90 b = 157.596 β = 90 c = 84.707 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
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 2.48 50 96.4 0.076 9.9 24570
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) 2.5 2.59 98.4 0.885 2455
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2.48 47.14 22909 1096 93.3 0.2 0.197 0.2462 0.255 0.2897 RANDOM 46.436
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] 0.25 0.44 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.56 r_dihedral_angle_4_deg 19.306 r_dihedral_angle_3_deg 18.078 r_dihedral_angle_1_deg 5.059 r_scangle_it 2.31 r_scbond_it 1.345 r_angle_refined_deg 1.268 r_mcangle_it 0.767 r_mcbond_it 0.454 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.56 r_dihedral_angle_4_deg 19.306 r_dihedral_angle_3_deg 18.078 r_dihedral_angle_1_deg 5.059 r_scangle_it 2.31 r_scbond_it 1.345 r_angle_refined_deg 1.268 r_mcangle_it 0.767 r_mcbond_it 0.454 r_nbtor_refined 0.309 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.188 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4842 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction