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Crystal structure of M tuberculosis Adenosine Kinase complexed with adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PKF apo MTB ADK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 290 Crystals were obtained in conditions containing 0.1 M HEPES-Na, pH 7.5 and 1.4 M trisodium citrate dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.32 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.9 α = 90 b = 71.9 β = 90 c = 110.8 γ = 120
Symmetry Space Group P 31 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 120 IMAGE PLATE RIGAKU RAXIS IV Osmic mirrors 2006-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.5412
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 1.9 62.66 97.84 0.04 24855 24855
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.949 97.33
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 apo MTB ADK 1.9 62.26 24855 1299 97.84 0.21935 0.21723 0.2201 0.25956 0.2577 RANDOM 41.134
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.423 r_dihedral_angle_4_deg 17.533 r_dihedral_angle_3_deg 13.83 r_dihedral_angle_1_deg 6.091 r_scangle_it 5.746 r_scbond_it 4.331 r_mcangle_it 3.308 r_mcbond_it 2.458 r_angle_refined_deg 1.336 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.423 r_dihedral_angle_4_deg 17.533 r_dihedral_angle_3_deg 13.83 r_dihedral_angle_1_deg 6.091 r_scangle_it 5.746 r_scbond_it 4.331 r_mcangle_it 3.308 r_mcbond_it 2.458 r_angle_refined_deg 1.336 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.226 r_symmetry_vdw_refined 0.204 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.101 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2444 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling PHASER phasing