☰ Navigation Tabs
Crystal structure of shikimate kinase of Mycobacterium tuberculosis complex with shikimate-3-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Ammonium sulphate
0.1 M Sodium acetate trihydrate
pH - 4.6
30% PEG 2000
Crystal Properties Matthews coefficient Solvent content 2.92 57.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.424 α = 90 b = 59.424 β = 90 c = 102.25 γ = 120
Symmetry Space Group P 31 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 273 PIXEL DECTRIS PILATUS 6M 2022-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.96546 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.72 46.011 96 0.063 0.067 0.022 0.99 18.8 9.1 21710 29.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.756 100 1.072 0.369 0.913 9.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2IYX 1.726 46.011 21704 1144 95.98 0.179 0.1761 0.1875 0.2222 0.2297 33.05
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] -0.003 -0.002 -0.003 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.407 r_dihedral_angle_3_deg 13.03 r_dihedral_angle_2_deg 11.865 r_lrange_it 11.305 r_lrange_other 11.262 r_scangle_it 7.24 r_scangle_other 7.085 r_dihedral_angle_1_deg 5.482 r_scbond_it 4.884 r_scbond_other 4.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.407 r_dihedral_angle_3_deg 13.03 r_dihedral_angle_2_deg 11.865 r_lrange_it 11.305 r_lrange_other 11.262 r_scangle_it 7.24 r_scangle_other 7.085 r_dihedral_angle_1_deg 5.482 r_scbond_it 4.884 r_scbond_other 4.624 r_mcangle_other 4.458 r_mcangle_it 4.456 r_mcbond_it 3.14 r_mcbond_other 3.112 r_angle_refined_deg 1.747 r_angle_other_deg 0.594 r_symmetry_nbd_refined 0.347 r_nbd_refined 0.246 r_nbd_other 0.211 r_xyhbond_nbd_refined 0.201 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.195 r_symmetry_xyhbond_nbd_refined 0.175 r_symmetry_xyhbond_nbd_other 0.109 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1252 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing