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Crystal structure of thymidylate kinase from thermus thermophilus HB8
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 295 0.2M CaCl2.2H2O, 20% w/v, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 47.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.47 α = 90 b = 80.21 β = 90 c = 122.63 γ = 90
Symmetry Space Group P 21 21 21
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 2012-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.83 40.88 96.8 0.095 0.997 12.8 8.6 34412
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 1.83 1.87 0.826
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 1.84 40.88 32679 1667 99.35 0.17831 0.17614 0.21996 0.2258 RANDOM 21.198
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] 0.4 0.45 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.627 r_dihedral_angle_4_deg 17.262 r_dihedral_angle_3_deg 12.878 r_long_range_B_refined 6.314 r_long_range_B_other 6.025 r_dihedral_angle_1_deg 5.895 r_scangle_other 4.085 r_mcangle_other 2.862 r_mcangle_it 2.861 r_scbond_it 2.653
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.627 r_dihedral_angle_4_deg 17.262 r_dihedral_angle_3_deg 12.878 r_long_range_B_refined 6.314 r_long_range_B_other 6.025 r_dihedral_angle_1_deg 5.895 r_scangle_other 4.085 r_mcangle_other 2.862 r_mcangle_it 2.861 r_scbond_it 2.653 r_scbond_other 2.645 r_mcbond_it 1.921 r_mcbond_other 1.917 r_angle_refined_deg 1.88 r_angle_other_deg 1.066 r_chiral_restr 0.117 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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 2975 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction Aimless data scaling PHASER phasing