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Structure of shikimate kinase from Mycobacterium tuberculosis complexed with ADP and shikimate at 1.9 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, 17% PEG 1500, 0.5-0.7M LiCl, pH 8.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.84 56.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.296 α = 90 b = 63.296 β = 90 c = 91.61 γ = 120
Symmetry Space Group P 32 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 IMAGE PLATE RIGAKU 2005-06-07 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 1.93 35.16 99 4.8 16169 16017 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) 1.93 2.03 21.6 4.6 2160
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 1.93 35.16 2 16475 15130 804 96.72 0.20494 0.202 0.2017 0.1991 0.26687 0.2657 RANDOM 32.718
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.012 r_dihedral_angle_3_deg 19.884 r_dihedral_angle_4_deg 19.472 r_scangle_it 9.333 r_dihedral_angle_1_deg 8.385 r_scbond_it 7.39 r_mcangle_it 4.917 r_mcbond_it 3.937 r_angle_refined_deg 2.01 r_symmetry_hbond_refined 0.555
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.012 r_dihedral_angle_3_deg 19.884 r_dihedral_angle_4_deg 19.472 r_scangle_it 9.333 r_dihedral_angle_1_deg 8.385 r_scbond_it 7.39 r_mcangle_it 4.917 r_mcbond_it 3.937 r_angle_refined_deg 2.01 r_symmetry_hbond_refined 0.555 r_xyhbond_nbd_refined 0.423 r_nbd_refined 0.361 r_symmetry_vdw_refined 0.35 r_nbtor_refined 0.319 r_chiral_restr 0.187 r_bond_refined_d 0.015 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1226 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing