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Citrate 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 MICROBATCH 7 295 0.2M Ammonium citrate tribasic, 20% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.46 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.76 α = 92.85 b = 51.53 β = 92.49 c = 53.25 γ = 112.63
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 2012-11-15 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) 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 2.03 53.06 91.3 0.999 16.1 3.9 24537 33.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.09 60.1 0.92 2.5 3.5 1170
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2PBR 2.05 53.06 23283 1251 93.13 0.21331 0.21015 0.27135 0.2475 RANDOM 36.369
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] -2.99 0.26 2.29 0.72 4.7 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.666 r_dihedral_angle_4_deg 20.848 r_dihedral_angle_3_deg 14.042 r_dihedral_angle_1_deg 5.922 r_long_range_B_other 4.484 r_long_range_B_refined 4.482 r_scangle_other 2.995 r_mcangle_other 2.692 r_mcangle_it 2.69 r_scbond_it 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.666 r_dihedral_angle_4_deg 20.848 r_dihedral_angle_3_deg 14.042 r_dihedral_angle_1_deg 5.922 r_long_range_B_other 4.484 r_long_range_B_refined 4.482 r_scangle_other 2.995 r_mcangle_other 2.692 r_mcangle_it 2.69 r_scbond_it 1.87 r_scbond_other 1.87 r_mcbond_it 1.702 r_mcbond_other 1.696 r_angle_refined_deg 1.285 r_angle_other_deg 0.922 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 3030 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing