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Crystal structure of thymidylate kinase in complex with ADP and TMP 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 CaCl2.2H2O, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.94 36.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.17 α = 90 b = 47.474 β = 90 c = 152.169 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 MAR scanner 345 mm plate 2013-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.5417
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.92 19.74 99.9 0.064 0.998 15.75 7 26814
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.95 0.168 0.983
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 1.92 19.74 25414 1314 99.42 0.19052 0.18827 0.1988 0.23268 0.239 RANDOM 15.586
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] 0.59 -0.83 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.013 r_dihedral_angle_4_deg 19.002 r_dihedral_angle_3_deg 13.239 r_dihedral_angle_1_deg 5.287 r_long_range_B_other 4.362 r_long_range_B_refined 4.361 r_scangle_other 2.208 r_mcangle_other 1.715 r_mcangle_it 1.714 r_angle_refined_deg 1.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.013 r_dihedral_angle_4_deg 19.002 r_dihedral_angle_3_deg 13.239 r_dihedral_angle_1_deg 5.287 r_long_range_B_other 4.362 r_long_range_B_refined 4.361 r_scangle_other 2.208 r_mcangle_other 1.715 r_mcangle_it 1.714 r_angle_refined_deg 1.684 r_scbond_it 1.355 r_scbond_other 1.334 r_mcbond_it 1.038 r_mcbond_other 1.032 r_angle_other_deg 0.987 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 2862 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing