☰ Navigation Tabs
Crystal structure (type-3) of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PLR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 293 0.01 M Magnesium chloride hexahydrate, 0.005 M Nickel(II) chloride hexahydrate, 0.1 M HEPES sodium, 15% w/v Polyethylene glycol 3,350, 0.5 M Sodium fluoride, pH 7.0, Microbatch Underoil, temperature 293.0K, EVAPORATION
Crystal Properties Matthews coefficient Solvent content 2.22 44.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.934 α = 90 b = 63.222 β = 90 c = 138.565 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS V RH Coated Bent-Cyrindrical MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 0.9000 SPring-8 BL26B2
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 2.3 50 99 0.09 19.348 7.2 20021
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 2.3 2.34 100 0.395 4.66 7.4
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 2PLR 2.3 50 18955 1031 98.92 0.20415 0.2011 0.2059 0.25903 0.2619 RANDOM 59.449
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] 3.06 -0.92 -2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.958 r_dihedral_angle_4_deg 20.815 r_dihedral_angle_3_deg 15.593 r_long_range_B_other 8.1 r_long_range_B_refined 8.099 r_scangle_other 6.125 r_dihedral_angle_1_deg 6.081 r_mcangle_other 5.353 r_mcangle_it 5.305 r_scbond_other 4.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.958 r_dihedral_angle_4_deg 20.815 r_dihedral_angle_3_deg 15.593 r_long_range_B_other 8.1 r_long_range_B_refined 8.099 r_scangle_other 6.125 r_dihedral_angle_1_deg 6.081 r_mcangle_other 5.353 r_mcangle_it 5.305 r_scbond_other 4.222 r_scbond_it 4.069 r_mcbond_it 3.76 r_mcbond_other 3.759 r_angle_refined_deg 1.695 r_angle_other_deg 0.855 r_chiral_restr 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3137 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 11
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling