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Human purine nucleoside phosphorylase double mutant E201Q,N243D complexed with 2-fluoroadenine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RFG PDB entry 1RFG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 1.54 M Ammonium sulfate, 0.05M Sodium potassium phosphate pH 6.8, 3% Trimethylamine N-oxide, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.39 63.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.791 α = 90 b = 130.648 β = 90 c = 149.177 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315 2008-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9793 APS 24-ID-C
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 81.2 0.105 16.923 5.8 51620 -3 52.4
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 26.8 0.336 5.4 1680
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1RFG 2.3 50 51499 2605 81.6 0.186 0.184 0.227 0.2394 RANDOM 32.774
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] 5.22 -2.57 -2.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.966 r_dihedral_angle_4_deg 18.949 r_dihedral_angle_3_deg 17.336 r_dihedral_angle_1_deg 6.189 r_scangle_it 3.637 r_mcangle_it 3.566 r_scbond_it 2.49 r_mcbond_it 2.168 r_angle_refined_deg 1.362 r_angle_other_deg 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.966 r_dihedral_angle_4_deg 18.949 r_dihedral_angle_3_deg 17.336 r_dihedral_angle_1_deg 6.189 r_scangle_it 3.637 r_mcangle_it 3.566 r_scbond_it 2.49 r_mcbond_it 2.168 r_angle_refined_deg 1.362 r_angle_other_deg 0.86 r_mcbond_other 0.525 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6452 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 204
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction