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Magnesium bound apo structure of thymidylate kinase (form I) 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 2.2 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.62 α = 90 b = 80.72 β = 90 c = 122.79 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 2012-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.541
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 48.87 97.2 0.103 0.998 14 10 26844
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 2 2.05
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 2.01 48.87 26777 1368 99.06 0.1773 0.1749 0.2224 0.2247 RANDOM 23.2332
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] -0.38 0.88 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.992 r_dihedral_angle_4_deg 19.661 r_dihedral_angle_3_deg 14.129 r_dihedral_angle_1_deg 5.628 r_angle_other_deg 3.593 r_mcangle_it 3.389 r_mcbond_it 2.15 r_mcbond_other 2.15 r_angle_refined_deg 1.833 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.992 r_dihedral_angle_4_deg 19.661 r_dihedral_angle_3_deg 14.129 r_dihedral_angle_1_deg 5.628 r_angle_other_deg 3.593 r_mcangle_it 3.389 r_mcbond_it 2.15 r_mcbond_other 2.15 r_angle_refined_deg 1.833 r_chiral_restr 0.1 r_bond_refined_d 0.018 r_gen_planes_other 0.012 r_gen_planes_refined 0.01 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2981 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction Aimless data scaling PHASER phasing