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Crystal structure of thymidylate kinase in complex with ADP, TDP and TMP 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, 0.1M Tris hydrochloride, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.07 40.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.408 α = 90 b = 47.658 β = 90 c = 152.329 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 2013-07-26 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 2.36 18.54 99.7 0.135 0.995 10.5 7 14849
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.36 2.46 0.453 0.847
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 5X7J 2.36 18.54 13923 688 98.29 0.2488 0.2451 0.3239 0.282 RANDOM 19.868
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] 1.23 -0.86 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.163 r_dihedral_angle_4_deg 16.572 r_dihedral_angle_3_deg 14.608 r_dihedral_angle_1_deg 5.18 r_angle_other_deg 3.604 r_mcangle_it 1.439 r_angle_refined_deg 1.349 r_mcbond_it 0.791 r_mcbond_other 0.789 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.163 r_dihedral_angle_4_deg 16.572 r_dihedral_angle_3_deg 14.608 r_dihedral_angle_1_deg 5.18 r_angle_other_deg 3.604 r_mcangle_it 1.439 r_angle_refined_deg 1.349 r_mcbond_it 0.791 r_mcbond_other 0.789 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2907 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction Aimless data scaling PHASER phasing