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Structure of shikimate kinase from Mycobacterium tuberculosis complexed with ADP and Mg at 2.8 angstrons of resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WE2 PDB ENTRY 1WE2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 293 0,1M tris HCl, pH 8.0, 25% PEG 3350 and 0,1M MgCl2, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.619 α = 90 b = 62.203 β = 90 c = 170.633 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU 2005-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.427 LNLS D03B-MX1
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 2.8 63.25 99.6 5.7 17130 17057 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.95 19.07
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1WE2 2.8 57.17 2 16548 15670 832 99.72 0.18806 0.183 0.18294 0.184 0.28162 0.2751 RANDOM 34.155
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] 0.54 -0.11 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.772 r_dihedral_angle_3_deg 22.639 r_dihedral_angle_4_deg 22.3 r_dihedral_angle_1_deg 11.859 r_scangle_it 11.064 r_scbond_it 10.281 r_mcbond_it 7.936 r_mcangle_it 7.517 r_angle_refined_deg 3.754 r_symmetry_hbond_refined 0.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.772 r_dihedral_angle_3_deg 22.639 r_dihedral_angle_4_deg 22.3 r_dihedral_angle_1_deg 11.859 r_scangle_it 11.064 r_scbond_it 10.281 r_mcbond_it 7.936 r_mcangle_it 7.517 r_angle_refined_deg 3.754 r_symmetry_hbond_refined 0.446 r_symmetry_vdw_refined 0.419 r_nbtor_refined 0.353 r_nbd_refined 0.343 r_xyhbond_nbd_refined 0.282 r_chiral_restr 0.242 r_metal_ion_refined 0.174 r_bond_refined_d 0.029 r_gen_planes_refined 0.023 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_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 4777 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing