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Crystal structure of ATP-TMP and ADP bound thymidylate kinase from Thermus thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X7J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 295 0.2M MgCl2.6H2O, 0.1 M Tris hydrochloride, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.93 36.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.058 α = 90 b = 47.467 β = 90 c = 152.453 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 CCD MARMOSAIC 225 mm CCD 2014-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9762 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.39 50.01 94.3 46.2 9.1 65283
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.39 1.42
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 5X7J 1.39 50.01 61892 3314 94.11 0.14578 0.14384 0.1436 0.18118 0.1811 RANDOM 16.725
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] 0.1 -0.24 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.718 r_sphericity_free 20.595 r_dihedral_angle_4_deg 18.727 r_dihedral_angle_3_deg 12.837 r_sphericity_bonded 8.391 r_dihedral_angle_1_deg 5.353 r_long_range_B_refined 2.951 r_long_range_B_other 2.951 r_scangle_other 2.522 r_scbond_it 2.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.718 r_sphericity_free 20.595 r_dihedral_angle_4_deg 18.727 r_dihedral_angle_3_deg 12.837 r_sphericity_bonded 8.391 r_dihedral_angle_1_deg 5.353 r_long_range_B_refined 2.951 r_long_range_B_other 2.951 r_scangle_other 2.522 r_scbond_it 2.014 r_scbond_other 2.014 r_mcangle_other 1.874 r_mcangle_it 1.873 r_angle_refined_deg 1.718 r_mcbond_it 1.458 r_mcbond_other 1.45 r_rigid_bond_restr 1.4 r_angle_other_deg 0.973 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2899 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Aimless data scaling PHASER phasing