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Crystal structure of TMP bound thymidylate kinase from thermus thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X7J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 295 0.2M MgCl2.6H2O, 0.1 M Tris hydrochloride, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.92 35.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.901 α = 90 b = 47.435 β = 90 c = 152.062 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 CCD MARMOSAIC 225 mm CCD 2014-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.8265 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.19 50.01 99 1.8 5.7 108625
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19 1.21
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 5X7J 1.19 50.01 103154 5368 99.07 0.14183 0.14053 0.1403 0.1679 0.1674 RANDOM 14.304
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] -0.57 0.29 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.269 r_sphericity_free 21.435 r_dihedral_angle_4_deg 19.932 r_dihedral_angle_3_deg 12.205 r_sphericity_bonded 9.991 r_dihedral_angle_1_deg 5.291 r_long_range_B_refined 3.297 r_long_range_B_other 3.098 r_scangle_other 2.819 r_scbond_it 2.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.269 r_sphericity_free 21.435 r_dihedral_angle_4_deg 19.932 r_dihedral_angle_3_deg 12.205 r_sphericity_bonded 9.991 r_dihedral_angle_1_deg 5.291 r_long_range_B_refined 3.297 r_long_range_B_other 3.098 r_scangle_other 2.819 r_scbond_it 2.296 r_scbond_other 2.285 r_mcangle_it 2.002 r_mcangle_other 2.002 r_angle_refined_deg 1.934 r_rigid_bond_restr 1.761 r_mcbond_it 1.515 r_mcbond_other 1.503 r_angle_other_deg 1.03 r_chiral_restr 0.113 r_bond_refined_d 0.014 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2907 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing