☰ Navigation Tabs
Crystal structure of adenosine deaminase from Plasmodium vivax in complex with pentostatin
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 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 3.03 59.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.488 α = 90 b = 146.386 β = 90 c = 50.034 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 2007-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91722 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 2.3 50 99.6 0.103 6.6 4.1 23772 23772 32.4
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 2.3 2.38 99.8 0.427 3.09 4.1 2375
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2PGF 2.3 37 23771 1171 99.54 0.171 0.171 0.168 0.22 RANDOM 16.985
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] 1.19 -1.77 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.483 r_dihedral_angle_3_deg 12.678 r_dihedral_angle_4_deg 10.601 r_dihedral_angle_1_deg 5.291 r_scangle_it 3.496 r_scbond_it 2.568 r_mcangle_it 1.715 r_mcbond_it 1.458 r_angle_refined_deg 0.883 r_angle_other_deg 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.483 r_dihedral_angle_3_deg 12.678 r_dihedral_angle_4_deg 10.601 r_dihedral_angle_1_deg 5.291 r_scangle_it 3.496 r_scbond_it 2.568 r_mcangle_it 1.715 r_mcbond_it 1.458 r_angle_refined_deg 0.883 r_angle_other_deg 0.78 r_mcbond_other 0.324 r_nbd_refined 0.186 r_symmetry_vdw_other 0.174 r_nbtor_refined 0.171 r_nbd_other 0.163 r_xyhbond_nbd_refined 0.126 r_symmetry_hbond_refined 0.102 r_metal_ion_refined 0.098 r_symmetry_vdw_refined 0.094 r_nbtor_other 0.08 r_chiral_restr 0.05 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 110 Heterogen Atoms 26
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 MOLREP phasing