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Crystal Structure of Trypanosoma brucei rhodesiense Adenosine Kinase Complexed with Inhibitor AP5A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BX4 PDB entry 1BX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.1M sodium citrate, 20% iso-propanol, 20% PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.893 α = 90 b = 70.549 β = 90.77 c = 72.41 γ = 90
Symmetry Space Group P 1 21 1
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 Mirrors 2007-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.55 80 96.5 0.054 14.6 3.8 97047 97047 -3 26.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.6 95.1 0.434 3.5 3.8 8658
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 1BX4 1.55 72.36 97047 92189 4858 96.49 0.1826 0.18093 0.19 0.21417 0.2219 RANDOM 24.354
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] 0.37 0.57 -0.15 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.614 r_dihedral_angle_4_deg 15.878 r_dihedral_angle_3_deg 13.084 r_scangle_it 7.16 r_dihedral_angle_1_deg 5.524 r_scbond_it 4.642 r_mcangle_it 3.148 r_mcbond_it 1.747 r_angle_refined_deg 1.485 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.614 r_dihedral_angle_4_deg 15.878 r_dihedral_angle_3_deg 13.084 r_scangle_it 7.16 r_dihedral_angle_1_deg 5.524 r_scbond_it 4.642 r_mcangle_it 3.148 r_mcbond_it 1.747 r_angle_refined_deg 1.485 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5253 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 116
Software Software Software Name Purpose PHASER phasing MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling