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Crystal structure of the Trypanosoma brucei Inosine-Adenosine-Guanosine nucleoside hydrolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KIC IAGNH-363
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.8 292 0.2M ammonium acetate, 18% PEG3350, pH 4.8, VAPOR DIFFUSION, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.01 38.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.04 α = 90 b = 48.04 β = 90 c = 216.11 γ = 120
Symmetry Space Group P 32 1 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 ADSC QUANTUM 315r 2010-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
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 1.6 72.037 99.7 0.099 22.52 9.8 38235 38235 -3 25.479
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 1.6 1.7 99.3 0.389 0.418 5.94 7.5 6215
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT IAGNH-363 1.6 72 38232 38232 1916 99.75 0.1438 0.1419 0.1817 0.1887 RANDOM 19.1117
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] -0.04 -0.02 -0.04 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.137 r_dihedral_angle_4_deg 15.319 r_dihedral_angle_3_deg 12.082 r_sphericity_free 7.293 r_dihedral_angle_1_deg 5.457 r_scangle_it 4.619 r_scbond_it 3.03 r_sphericity_bonded 2.947 r_mcangle_it 2.052 r_angle_refined_deg 1.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.137 r_dihedral_angle_4_deg 15.319 r_dihedral_angle_3_deg 12.082 r_sphericity_free 7.293 r_dihedral_angle_1_deg 5.457 r_scangle_it 4.619 r_scbond_it 3.03 r_sphericity_bonded 2.947 r_mcangle_it 2.052 r_angle_refined_deg 1.541 r_rigid_bond_restr 1.429 r_mcbond_it 1.305 r_angle_other_deg 0.996 r_mcbond_other 0.542 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2420 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 1
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection XDS data reduction