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Phosphate ion 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 EVAPORATION 7.5 293 0.1 M HEPES, 10% w/v Polyethylene glycol 8,000,
8% v/v Ethylene glycol , Microbatch Underoil, pH 7.5, EVAPORATION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.87 α = 92.29 b = 51.78 β = 92.83 c = 53.65 γ = 112.76
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 Mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 2.35 40 90.4 0.05 18.5 4 63136 15954 33
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 2.35 2.48 92.3 0.118 9.6 4 9345
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 2.35 40 15094 826 90.17 0.20377 0.20033 0.2072 0.26664 0.2672 RANDOM 32.711
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] -2.69 0.57 2.07 0.27 4.44 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.12 r_dihedral_angle_4_deg 21.785 r_dihedral_angle_3_deg 14.686 r_dihedral_angle_1_deg 6.044 r_long_range_B_refined 5.434 r_long_range_B_other 5.434 r_scangle_other 3.977 r_mcangle_it 3.461 r_mcangle_other 3.461 r_scbond_it 2.581
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.12 r_dihedral_angle_4_deg 21.785 r_dihedral_angle_3_deg 14.686 r_dihedral_angle_1_deg 6.044 r_long_range_B_refined 5.434 r_long_range_B_other 5.434 r_scangle_other 3.977 r_mcangle_it 3.461 r_mcangle_other 3.461 r_scbond_it 2.581 r_scbond_other 2.555 r_mcbond_other 2.322 r_mcbond_it 2.321 r_angle_refined_deg 1.523 r_angle_other_deg 0.847 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2987 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 10
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling