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Catalytic domain of protein kinase PknB from Mycobacterium tuberculosis in complex with mitoxantrone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O6Y PDB ENTRY 1O6Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 1.2M NaAcetate
50mM NaCacodylate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.42 64.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.863 α = 90 b = 116.863 β = 90 c = 260.347 γ = 90
Symmetry Space Group P 43 21 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 MARRESEARCH 2005-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.89 69.84 63.47 28195 28195 1 1
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 2.89 3.21 16
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1O6Y 2.89 69.84 26685 26685 1426 68.13 0.22097 0.21784 0.2138 0.27798 0.2765 RANDOM 79.784
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] 3.91 3.91 -7.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.069 r_dihedral_angle_3_deg 24.322 r_dihedral_angle_4_deg 20.695 r_dihedral_angle_1_deg 7.212 r_scangle_it 2.074 r_angle_refined_deg 1.737 r_scbond_it 1.14 r_mcangle_it 0.566 r_nbtor_refined 0.325 r_mcbond_it 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.069 r_dihedral_angle_3_deg 24.322 r_dihedral_angle_4_deg 20.695 r_dihedral_angle_1_deg 7.212 r_scangle_it 2.074 r_angle_refined_deg 1.737 r_scbond_it 1.14 r_mcangle_it 0.566 r_nbtor_refined 0.325 r_mcbond_it 0.319 r_nbd_refined 0.266 r_symmetry_vdw_refined 0.244 r_xyhbond_nbd_refined 0.182 r_symmetry_hbond_refined 0.181 r_chiral_restr 0.127 r_bond_refined_d 0.015 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 7870 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing