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Crystal structure of adenosine deaminase from Plasmodium vivax in complex with guanosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PGF PDB entry 2PGF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 27.3% PEG 20000, 0.1 M CHES pH 9.5, 0.1 M Sodium phosphate monobasic, 5 mM Guanosine, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.08 60.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.548 α = 90 b = 146.922 β = 90 c = 50.453 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 2007-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837 SSRL BL11-1
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 2.19 40 99.6 0.146 5.6 6.6 27968 27968 30.2
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 2.19 2.28 97.1 0.678 1.7 5 2662
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 2PGF 2.19 35 27942 27942 1404 98.94 0.175 0.175 0.172 0.1834 0.232 0.2335 RANDOM 29.408
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] 1.8 -2.19 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.164 r_dihedral_angle_4_deg 20.21 r_dihedral_angle_3_deg 12.769 r_scangle_it 5.854 r_dihedral_angle_1_deg 5.344 r_scbond_it 4.349 r_mcangle_it 2.686 r_mcbond_it 2.067 r_angle_refined_deg 1.043 r_angle_other_deg 0.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.164 r_dihedral_angle_4_deg 20.21 r_dihedral_angle_3_deg 12.769 r_scangle_it 5.854 r_dihedral_angle_1_deg 5.344 r_scbond_it 4.349 r_mcangle_it 2.686 r_mcbond_it 2.067 r_angle_refined_deg 1.043 r_angle_other_deg 0.825 r_mcbond_other 0.368 r_symmetry_vdw_other 0.27 r_nbd_refined 0.19 r_nbtor_refined 0.173 r_nbd_other 0.17 r_xyhbond_nbd_refined 0.126 r_symmetry_hbond_refined 0.094 r_symmetry_vdw_refined 0.085 r_nbtor_other 0.083 r_chiral_restr 0.059 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 2923 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 33
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing