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Shikimate kinase from Mycobacterium tuberculosis in complex with shikimate-3-phosphate and SO4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IYX PDB ENTRY 2IYX
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 50.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.349 α = 90 b = 59.349 β = 90 c = 102.867 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 2005-08-10 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 1.62 19.16 93.8 0.06 5.7 2.31 25604
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 1.62 1.66 92.5 0.95 1.4 2.2
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 2IYX 1.62 19.16 24283 1321 93.8 0.178 0.175 0.1872 0.233 0.2378 RANDOM 24.6
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] 1.41 0.7 1.41 -2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.038 r_dihedral_angle_4_deg 16.139 r_dihedral_angle_3_deg 15.153 r_scangle_it 13.474 r_scbond_it 10.359 r_mcangle_it 6.137 r_mcbond_it 6.022 r_dihedral_angle_1_deg 5.697 r_angle_refined_deg 1.651 r_angle_other_deg 0.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.038 r_dihedral_angle_4_deg 16.139 r_dihedral_angle_3_deg 15.153 r_scangle_it 13.474 r_scbond_it 10.359 r_mcangle_it 6.137 r_mcbond_it 6.022 r_dihedral_angle_1_deg 5.697 r_angle_refined_deg 1.651 r_angle_other_deg 0.905 r_symmetry_vdw_other 0.283 r_nbd_refined 0.219 r_nbd_other 0.212 r_xyhbond_nbd_refined 0.19 r_symmetry_vdw_refined 0.178 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.167 r_chiral_restr 0.102 r_nbtor_other 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.004 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 1258 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling