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AMPPCP and TMP 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 pdb entry 2PBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 293 0.1 NaAcetate pH 5.4, 0.2 M
MgFormate,10 mM dTMP, 10mM AMP-PCP, 10 mM MgCl2, 20% Glycerol as cryoprotectant, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.479 α = 90 b = 62.615 β = 97.97 c = 73.577 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 RH Coated Bent-Cyrindrical MIRROR 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 1.55 50 98.61 0.047 33.59 7.1 390513 54781 13.4
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 1.55 1.61 90.4 0.158 9.376 5.3 5025
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 2PBR 1.55 50 390513 51970 2809 98.6 0.14778 0.14632 0.1457 0.17413 0.1739 RANDOM 14.789
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] -0.77 -0.13 1.39 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.423 r_dihedral_angle_4_deg 17.223 r_dihedral_angle_3_deg 12.157 r_dihedral_angle_1_deg 6.107 r_long_range_B_refined 5.468 r_long_range_B_other 5.265 r_scangle_other 3.848 r_scbond_it 2.568 r_scbond_other 2.563 r_angle_refined_deg 2.473
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.423 r_dihedral_angle_4_deg 17.223 r_dihedral_angle_3_deg 12.157 r_dihedral_angle_1_deg 6.107 r_long_range_B_refined 5.468 r_long_range_B_other 5.265 r_scangle_other 3.848 r_scbond_it 2.568 r_scbond_other 2.563 r_angle_refined_deg 2.473 r_mcangle_it 2.454 r_mcangle_other 2.454 r_mcbond_it 1.675 r_mcbond_other 1.674 r_angle_other_deg 1.026 r_chiral_restr 0.145 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3071 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 117
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling