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Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with 2-fluoroadenosine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 291 0.1 M sodium acetate, 3.2 M sodium chloride, 5%(v/v) glycerol, pH 4.6, vapor diffusion, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.66 53.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.804 α = 90 b = 135.804 β = 90 c = 55.154 γ = 120
Symmetry Space Group P 3 2 1
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 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.56 40 93.7 0.104 12.3 4.4 17770 17770
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.56 2.7 93.7 0.303 0.303 2.1 4.4 2561
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.56 20 17733 943 92.8 0.1596 0.1566 0.211 0.2367 RANDOM 23.5882
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] -12.58 -12.58 25.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.958 r_dihedral_angle_3_deg 14.896 r_dihedral_angle_4_deg 14.161 r_dihedral_angle_1_deg 6.836 r_scangle_it 2.62 r_scbond_it 1.584 r_angle_refined_deg 1.407 r_mcangle_it 1.117 r_angle_other_deg 0.888 r_mcbond_it 0.588
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.958 r_dihedral_angle_3_deg 14.896 r_dihedral_angle_4_deg 14.161 r_dihedral_angle_1_deg 6.836 r_scangle_it 2.62 r_scbond_it 1.584 r_angle_refined_deg 1.407 r_mcangle_it 1.117 r_angle_other_deg 0.888 r_mcbond_it 0.588 r_mcbond_other 0.095 r_chiral_restr 0.071 r_bond_refined_d 0.013 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3509 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 40
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction