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Shikimate kinase from Mycobacterium tuberculosis in complex with shikimate and SO4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IYQ PDB ENTRY 2IYQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 200MM MGSO4, 20%(W/V) PEG 3350, pH 8.00
Crystal Properties Matthews coefficient Solvent content 2.5 50.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.245 α = 90 b = 59.245 β = 90 c = 102.797 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 100 CCD MARRESEARCH MIRRORS 2005-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 MPG/DESY, HAMBURG BW6
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 1.49 19.51 99.4 0.04 12.69 3.04 34443
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) 1 1.49 1.53 98.7 0.41 2.17 3
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 PDB ENTRY 2IYQ 1.49 19.51 32698 1746 99.4 0.168 0.167 0.1756 0.206 0.2093 RANDOM 18.75
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] 1.05 0.52 1.05 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.549 r_dihedral_angle_4_deg 15.013 r_dihedral_angle_3_deg 13.524 r_scangle_it 13.519 r_scbond_it 10.804 r_mcbond_it 6.397 r_mcangle_it 6.231 r_dihedral_angle_1_deg 5.317 r_angle_refined_deg 1.795 r_angle_other_deg 0.942
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.549 r_dihedral_angle_4_deg 15.013 r_dihedral_angle_3_deg 13.524 r_scangle_it 13.519 r_scbond_it 10.804 r_mcbond_it 6.397 r_mcangle_it 6.231 r_dihedral_angle_1_deg 5.317 r_angle_refined_deg 1.795 r_angle_other_deg 0.942 r_symmetry_vdw_other 0.297 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.237 r_nbd_other 0.206 r_symmetry_hbond_refined 0.182 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.106 r_nbtor_other 0.083 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1253 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing