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Crystal structure of thymidylate kinase in complex with ADP and TDP 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, 0.1M Tris hydrochloride, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.92 35.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.871 α = 90 b = 47.385 β = 90 c = 151.987 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 0.9537 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.19 50.01 98.4 0.026 0.9818 37.12 4 107494
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19 1.21 0.203 0.855
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 1.19 50.01 102018 5401 99.12 0.13006 0.12882 0.1286 0.1529 0.1523 RANDOM 12.357
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] 0.11 -0.14 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.456 r_sphericity_free 19.842 r_dihedral_angle_4_deg 19.176 r_dihedral_angle_3_deg 11.285 r_sphericity_bonded 6.899 r_dihedral_angle_1_deg 5.136 r_long_range_B_refined 2.363 r_long_range_B_other 2.128 r_scangle_other 2.019 r_angle_refined_deg 1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.456 r_sphericity_free 19.842 r_dihedral_angle_4_deg 19.176 r_dihedral_angle_3_deg 11.285 r_sphericity_bonded 6.899 r_dihedral_angle_1_deg 5.136 r_long_range_B_refined 2.363 r_long_range_B_other 2.128 r_scangle_other 2.019 r_angle_refined_deg 1.85 r_scbond_it 1.66 r_scbond_other 1.66 r_mcangle_it 1.431 r_mcangle_other 1.43 r_rigid_bond_restr 1.429 r_mcbond_it 1.03 r_mcbond_other 1.023 r_angle_other_deg 0.98 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 2866 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing