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ADP and dTDP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M Bis-Tris pH 6.5, 45% MPD, 0.2M CaCl2, 10mM Mg, 10mM dTDP, 10mM ADP
Crystal Properties Matthews coefficient Solvent content 2.25 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.482 α = 90 b = 62.414 β = 91.02 c = 76.144 γ = 90
Symmetry Space Group P 1 21 1
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 2007-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000 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 1.7 50 97.8 0.054 45.6 7 42940 22.6
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 1.7 1.76 82.3 0.159 7.51 4.2 3578
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 2PBR 1.7 50 40793 2127 97.78 0.15736 0.15589 0.169 0.18525 0.1932 RANDOM 14.244
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 -0.35 1.02 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.205 r_dihedral_angle_4_deg 17.36 r_dihedral_angle_3_deg 11.813 r_dihedral_angle_1_deg 5.161 r_long_range_B_refined 3.862 r_long_range_B_other 3.862 r_scangle_other 2.25 r_angle_refined_deg 1.569 r_mcangle_other 1.429 r_mcangle_it 1.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.205 r_dihedral_angle_4_deg 17.36 r_dihedral_angle_3_deg 11.813 r_dihedral_angle_1_deg 5.161 r_long_range_B_refined 3.862 r_long_range_B_other 3.862 r_scangle_other 2.25 r_angle_refined_deg 1.569 r_mcangle_other 1.429 r_mcangle_it 1.428 r_scbond_it 1.422 r_scbond_other 1.422 r_angle_other_deg 0.911 r_mcbond_it 0.875 r_mcbond_other 0.869 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 3073 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing