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Shikimate kinase from Mycobacterium tuberculosis in unliganded state, 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 31.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.192 α = 90 b = 44.192 β = 90 c = 152.628 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 ADSC CCD MIRRORS 2005-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.47 19.73 97.6 0.1 7.15 4.05 26142
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 1.47 1.51 98.7 0.72 2.04 4
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 2IYS 1.47 19.73 24844 1298 97.6 0.199 0.197 0.2019 0.246 0.2477 RANDOM 20.54
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] -0.08 -0.08 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.553 r_dihedral_angle_4_deg 17.585 r_scangle_it 16.113 r_dihedral_angle_3_deg 14.959 r_scbond_it 14.15 r_mcangle_it 6.532 r_dihedral_angle_1_deg 5.165 r_mcbond_it 4.99 r_angle_other_deg 3.571 r_angle_refined_deg 1.766
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.553 r_dihedral_angle_4_deg 17.585 r_scangle_it 16.113 r_dihedral_angle_3_deg 14.959 r_scbond_it 14.15 r_mcangle_it 6.532 r_dihedral_angle_1_deg 5.165 r_mcbond_it 4.99 r_angle_other_deg 3.571 r_angle_refined_deg 1.766 r_symmetry_vdw_other 0.332 r_nbd_other 0.233 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.228 r_symmetry_hbond_refined 0.188 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.117 r_nbtor_other 0.102 r_bond_refined_d 0.021 r_gen_planes_other 0.011 r_gen_planes_refined 0.009 r_bond_other_d 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 1293 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling