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Shikimate kinase from Mycobacterium tuberculosis in complex with shikimate
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 8.5 170MM NA ACETATE, 15%(V/V) GLYCEROL, 25.5%(W/V) PEG 4000, 85MM TRIS-HCL PH 8.5
Crystal Properties Matthews coefficient Solvent content 1.8 32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.444 α = 90 b = 41.836 β = 113.99 c = 44.408 γ = 90
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 2006-02-17 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 1.98 19.54 96.1 0.1 5.97 2.2 19559
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 1.98 2.03 92.9 0.61 1.48 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 2IYQ 1.98 41.85 18573 986 96.1 0.169 0.165 0.1759 0.25 0.2549 RANDOM 27.61
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] -0.76 -0.03 0.63 0.87 -0.78 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.321 r_dihedral_angle_4_deg 17.873 r_dihedral_angle_3_deg 17.104 r_scangle_it 11.432 r_scbond_it 8.883 r_dihedral_angle_1_deg 5.842 r_mcangle_it 5.246 r_mcbond_it 4.745 r_angle_refined_deg 1.597 r_angle_other_deg 0.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.321 r_dihedral_angle_4_deg 17.873 r_dihedral_angle_3_deg 17.104 r_scangle_it 11.432 r_scbond_it 8.883 r_dihedral_angle_1_deg 5.842 r_mcangle_it 5.246 r_mcbond_it 4.745 r_angle_refined_deg 1.597 r_angle_other_deg 0.885 r_symmetry_vdw_other 0.293 r_symmetry_hbond_refined 0.229 r_nbd_refined 0.225 r_nbd_other 0.201 r_xyhbond_nbd_refined 0.187 r_symmetry_vdw_refined 0.183 r_nbtor_refined 0.169 r_chiral_restr 0.09 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 2457 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing