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Crystal structure of M tuberculosis Adenosine Kinase (apo)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Se-met MAD low resolution structure
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 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.272 α = 90 b = 75.184 β = 121.05 c = 94.73 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 100 CCD MARMOSAIC 300 mm CCD 2005-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.979 APS 23-ID-B
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 1.5 81.11 99.77 0.04 104080 104080
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 1.5 1.53 99
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 Se-met MAD low resolution structure 1.5 81.11 104080 5485 99.77 0.17615 0.17497 0.1751 0.19831 0.1985 RANDOM 18.532
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] 0.47 0.91 -0.11 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.821 r_dihedral_angle_4_deg 20.797 r_dihedral_angle_3_deg 11.347 r_dihedral_angle_1_deg 5.803 r_scangle_it 3.196 r_scbond_it 2.065 r_mcangle_it 1.174 r_angle_refined_deg 1.171 r_mcbond_it 0.88 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.821 r_dihedral_angle_4_deg 20.797 r_dihedral_angle_3_deg 11.347 r_dihedral_angle_1_deg 5.803 r_scangle_it 3.196 r_scbond_it 2.065 r_mcangle_it 1.174 r_angle_refined_deg 1.171 r_mcbond_it 0.88 r_nbtor_refined 0.304 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.19 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 4989 Nucleic Acid Atoms Solvent Atoms 1106 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing