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Crystal structure of adenosine deaminase from Plasmodium vivax in complex with adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AMX PDB entry 2AMX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 33% PEG 20000, 0.1 M TAPS (pH 9.0), 0.1 M Sodium phosphate (monobasic), 16% acetonitrile, 5 mM adenosine, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.06 59.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.962 α = 90 b = 146.608 β = 90 c = 50.398 γ = 90
Symmetry Space Group C 2 2 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 CCD MARMOSAIC 325 mm CCD mirrors 2007-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97943 SSRL BL9-2
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 1.89 35 99.2 0.073 10.3 7.6 42835 42835 24.8
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 1.89 1.97 94.6 0.473 2.35 5.6 4009
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 (All) 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 2AMX 1.89 35 42786 42786 2144 98.36 0.15903 0.15903 0.15697 0.1589 0.20061 0.1997 RANDOM 21.575
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] 1.11 -2.13 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.375 r_dihedral_angle_4_deg 16.09 r_dihedral_angle_3_deg 11.491 r_dihedral_angle_1_deg 5.34 r_scangle_it 4.332 r_scbond_it 3.319 r_mcangle_it 2.127 r_mcbond_it 1.871 r_angle_refined_deg 1.058 r_angle_other_deg 0.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.375 r_dihedral_angle_4_deg 16.09 r_dihedral_angle_3_deg 11.491 r_dihedral_angle_1_deg 5.34 r_scangle_it 4.332 r_scbond_it 3.319 r_mcangle_it 2.127 r_mcbond_it 1.871 r_angle_refined_deg 1.058 r_angle_other_deg 0.806 r_mcbond_other 0.507 r_symmetry_vdw_other 0.243 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.202 r_nbtor_refined 0.175 r_nbd_other 0.17 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.118 r_nbtor_other 0.083 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2915 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing