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Crystal structure of the Trypanosoma brucei Inosine-Adenosine-Guanosine nucleoside hydrolase in complex with the NiTris metalorganic complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I71 TbbIAGNH-363 complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.6 292 0.1M Tris, 23% PEGMME2000, 10mM Ni2SO4, pH 8.6, VAPOR DIFFUSION, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.01 38.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.7 α = 90 b = 134.89 β = 90 c = 60.99 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 225 mm CCD 2010-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2
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 1.8 68 99.4 0.068 14.29 3.7 54442 54442 -3 25.787
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 94.7 0.561 0.66 2.6 3.5 3780
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 TbbIAGNH-363 complex 1.8 48.8 54442 54442 2761 99.4 0.1825 0.1804 0.197 0.2232 0.2357 RANDOM 20.222
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] 0.74 -0.96 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.025 r_dihedral_angle_4_deg 17.141 r_dihedral_angle_3_deg 15.04 r_sphericity_free 14.508 r_dihedral_angle_1_deg 6.243 r_scangle_it 3.979 r_scbond_it 2.577 r_angle_refined_deg 1.608 r_mcangle_it 1.437 r_angle_other_deg 1.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.025 r_dihedral_angle_4_deg 17.141 r_dihedral_angle_3_deg 15.04 r_sphericity_free 14.508 r_dihedral_angle_1_deg 6.243 r_scangle_it 3.979 r_scbond_it 2.577 r_angle_refined_deg 1.608 r_mcangle_it 1.437 r_angle_other_deg 1.164 r_mcbond_it 0.807 r_mcbond_other 0.272 r_chiral_restr 0.101 r_bond_refined_d 0.019 r_bond_other_d 0.004 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4972 Nucleic Acid Atoms Solvent Atoms 492 Heterogen Atoms 51
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection XDS data reduction