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Leishmania major Thymidine Kinase in complex with AP5dT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.1 M TRI-SODIUM CITRATE PH 5.5, 20 % (W/V) PEG 3000, 1 MM AP5DT, 1 MM DTHD, 1 MM APPNHP, 3 MM MGCL2
Crystal Properties Matthews coefficient Solvent content 2.19 43.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.149 α = 90 b = 64.149 β = 90 c = 324.6 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 45.84 99.9 0.12 11 8.2 16728 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 99.6 0.69 2.7 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.4 55.55 15762 829 99.59 0.19839 0.19546 0.25694 0.2357 RANDOM 49.68
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] 0.79 0.39 0.79 -2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.416 r_dihedral_angle_4_deg 17.422 r_dihedral_angle_3_deg 13.719 r_long_range_B_refined 6.392 r_long_range_B_other 6.391 r_dihedral_angle_1_deg 5.88 r_scangle_other 4.532 r_scbond_it 3.141 r_scbond_other 3.14 r_mcangle_it 3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.416 r_dihedral_angle_4_deg 17.422 r_dihedral_angle_3_deg 13.719 r_long_range_B_refined 6.392 r_long_range_B_other 6.391 r_dihedral_angle_1_deg 5.88 r_scangle_other 4.532 r_scbond_it 3.141 r_scbond_other 3.14 r_mcangle_it 3.09 r_mcangle_other 3.089 r_mcbond_it 1.904 r_mcbond_other 1.903 r_angle_refined_deg 1.694 r_angle_other_deg 1.027 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 2592 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing