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Crystal structure of M tuberculosis Adenosine Kinase complexed with AMP-PCP (non-hydrolyzable ATP analog)
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 6.5 290 20% PEG 8000, 100 mM sodium cacodylate pH 6.5, and 200 mM magnesium acetate tetrahydrate , VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.47 50.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.05 α = 90 b = 75.184 β = 109.8 c = 52.38 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 120 IMAGE PLATE RIGAKU RAXIS IV 2006-11-15 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 57.54 99.87 0.05 25991 25991
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 57.54 25991 1379 99.87 0.2095 0.20686 0.2038 0.25781 0.2509 RANDOM 34.41
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] -1.68 -1.11 1.04 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.088 r_dihedral_angle_4_deg 20.99 r_dihedral_angle_3_deg 13.871 r_dihedral_angle_1_deg 6.218 r_scangle_it 6.024 r_scbond_it 4.389 r_mcangle_it 3.367 r_mcbond_it 2.486 r_angle_refined_deg 1.275 r_symmetry_hbond_refined 0.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.088 r_dihedral_angle_4_deg 20.99 r_dihedral_angle_3_deg 13.871 r_dihedral_angle_1_deg 6.218 r_scangle_it 6.024 r_scbond_it 4.389 r_mcangle_it 3.367 r_mcbond_it 2.486 r_angle_refined_deg 1.275 r_symmetry_hbond_refined 0.377 r_nbtor_refined 0.293 r_symmetry_vdw_refined 0.25 r_nbd_refined 0.185 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2400 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement