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Crystal structure (form II) 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 MICROBATCH 295 CsCl2.H2O, 30% PEG 3500
Crystal Properties Matthews coefficient Solvent content 2.04 33.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.16 α = 90 b = 47.09 β = 90 c = 150.94 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 2013-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9737 ESRF BM14
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 1.5 25.16 99.9 0.097 0.998 10.6 7.6 53700 15.9
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 1.5 1.53
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 1.5 25.16 50895 2728 99.86 0.14529 0.14303 0.1887 0.214 RANDOM 22.238
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] -0.5 -0.89 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.913 r_sphericity_free 28.409 r_dihedral_angle_4_deg 17.763 r_sphericity_bonded 12.974 r_dihedral_angle_3_deg 12.795 r_dihedral_angle_1_deg 5.27 r_long_range_B_refined 4.475 r_long_range_B_other 4.392 r_scangle_other 4.184 r_scbond_it 3.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.913 r_sphericity_free 28.409 r_dihedral_angle_4_deg 17.763 r_sphericity_bonded 12.974 r_dihedral_angle_3_deg 12.795 r_dihedral_angle_1_deg 5.27 r_long_range_B_refined 4.475 r_long_range_B_other 4.392 r_scangle_other 4.184 r_scbond_it 3.41 r_scbond_other 3.409 r_mcangle_other 3.151 r_mcangle_it 3.143 r_mcbond_it 2.438 r_mcbond_other 2.423 r_rigid_bond_restr 2.212 r_angle_refined_deg 1.728 r_angle_other_deg 1.03 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2786 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing