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Crystal structure of shikimate kinase from Mycobacterium tuberculosis in complex with AMP-PNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZYU PDB ENTRY 1ZYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 293 PEG, pH8, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.43 64.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.297 α = 90 b = 67.297 β = 90 c = 97.692 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 CCD MAR CCD 165 mm 2007-04-17 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) R Merge I (Observed) R Sym 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 2.25 37.42 99.8 0.19 0.13 25.8 3.5 12600 2 2 35.1
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) 2.25 2.37 100 0.19 3.4 1816
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ZYU 2.25 37.42 2 12580 11983 597 99.72 0.21009 0.20651 0.28397 0.271 RANDOM 34.889
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] 0.82 0.41 0.82 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.229 r_dihedral_angle_4_deg 20.338 r_dihedral_angle_3_deg 18.056 r_dihedral_angle_1_deg 7.849 r_scangle_it 5.828 r_scbond_it 4.041 r_angle_refined_deg 3.034 r_mcbond_it 2.351 r_mcangle_it 2.348 r_symmetry_hbond_refined 0.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.229 r_dihedral_angle_4_deg 20.338 r_dihedral_angle_3_deg 18.056 r_dihedral_angle_1_deg 7.849 r_scangle_it 5.828 r_scbond_it 4.041 r_angle_refined_deg 3.034 r_mcbond_it 2.351 r_mcangle_it 2.348 r_symmetry_hbond_refined 0.526 r_xyhbond_nbd_refined 0.377 r_nbtor_refined 0.277 r_nbd_refined 0.223 r_chiral_restr 0.189 r_symmetry_vdw_refined 0.179 r_bond_refined_d 0.039 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1226 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling AMoRE phasing