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Shikimate kinase from Mycobacterium tuberculosis in complex with ADP, open LID (conf. A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IYS PDB ENTRY 2IYS
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 30.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.306 α = 90 b = 44.306 β = 90 c = 150.076 γ = 90
Symmetry Space Group P 43 21 2
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 MORRORS 2005-09-24 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 1.85 19.81 98 0.09 9.38 4.67 13255
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 1.85 1.9 99.5 0.88 2.05 4.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2IYS 1.85 19.81 12575 680 98 0.218 0.214 0.295 0.2936 RANDOM 26.35
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] -0.22 -0.22 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.965 r_dihedral_angle_3_deg 16.416 r_dihedral_angle_4_deg 16.184 r_scangle_it 14.451 r_scbond_it 12.443 r_mcangle_it 7.732 r_mcbond_it 7.12 r_dihedral_angle_1_deg 5.703 r_angle_refined_deg 1.849 r_angle_other_deg 0.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.965 r_dihedral_angle_3_deg 16.416 r_dihedral_angle_4_deg 16.184 r_scangle_it 14.451 r_scbond_it 12.443 r_mcangle_it 7.732 r_mcbond_it 7.12 r_dihedral_angle_1_deg 5.703 r_angle_refined_deg 1.849 r_angle_other_deg 0.915 r_symmetry_vdw_other 0.287 r_nbd_refined 0.218 r_nbd_other 0.21 r_xyhbond_nbd_refined 0.2 r_symmetry_hbond_refined 0.183 r_nbtor_refined 0.174 r_symmetry_vdw_refined 0.135 r_chiral_restr 0.1 r_nbtor_other 0.088 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 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 1241 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling