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ATP and CMP 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 7.5 293 0.1M HEPES, 10% w/v Polyethylene glycol 8000, 8% v/v Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.45 49.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.84 α = 92 b = 51.863 β = 92.3 c = 53.595 γ = 112.22
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 2012-12-06 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 2.3 30 98.8 0.142 6.83 3.9 18641 39.5
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 2.3 2.34 98.2 0.532 2.21 3.3
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 2.3 30 17588 939 97.93 0.19743 0.19449 0.1996 0.25109 0.2468 RANDOM 39.468
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] -2.94 0.78 2.41 1.31 4.65 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.313 r_dihedral_angle_4_deg 17.221 r_dihedral_angle_3_deg 15.026 r_long_range_B_refined 6.071 r_long_range_B_other 6.071 r_dihedral_angle_1_deg 6.07 r_scangle_other 4.645 r_mcangle_it 3.773 r_mcangle_other 3.772 r_scbond_it 3.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.313 r_dihedral_angle_4_deg 17.221 r_dihedral_angle_3_deg 15.026 r_long_range_B_refined 6.071 r_long_range_B_other 6.071 r_dihedral_angle_1_deg 6.07 r_scangle_other 4.645 r_mcangle_it 3.773 r_mcangle_other 3.772 r_scbond_it 3.115 r_scbond_other 3.108 r_mcbond_it 2.508 r_mcbond_other 2.508 r_angle_refined_deg 1.669 r_angle_other_deg 0.968 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2986 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing