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Crystal structure of shikimate kinase from Arabidopsis thaliana (AtSK2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2SHK PDB ENTRY 2SHK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 22% polyethylene glycol 3350, 0.2 M potassium fluoride, 3% 2-methyl-2,4-pentanediol, 1 mM magnesium chloride, 1 mM adenosine triphosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2 38.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.378 α = 90 b = 62.249 β = 90 c = 40.732 γ = 90
Symmetry Space Group P 21 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 QUANTUM 315 2009-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
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 2.35 19 89.8 0.119 0.107 13.3 5.4 16917 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.48 91.6 0.62 0.56 5.1 5
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 2SHK 2.35 19 16021 881 87.74 0.19433 0.19144 0.1956 0.2457 0.2503 RANDOM 18.974
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 1.31 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.651 r_dihedral_angle_3_deg 19.041 r_dihedral_angle_4_deg 16.949 r_dihedral_angle_1_deg 6.086 r_scangle_it 4.742 r_scbond_it 2.917 r_angle_refined_deg 1.72 r_mcangle_it 1.707 r_mcbond_it 0.892 r_chiral_restr 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.651 r_dihedral_angle_3_deg 19.041 r_dihedral_angle_4_deg 16.949 r_dihedral_angle_1_deg 6.086 r_scangle_it 4.742 r_scbond_it 2.917 r_angle_refined_deg 1.72 r_mcangle_it 1.707 r_mcbond_it 0.892 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3038 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling