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Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with tubercidin
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 2.77 55.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.638 α = 90 b = 135.638 β = 90 c = 57.56 γ = 120
Symmetry Space Group P 63 2 2
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 3.15 117.466 99.8 0.116 10.5 5.3 5743 5743
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 3.15 3.32 100 0.34 0.34 2 5.4 812
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.15 20 5713 260 99.65 0.2193 0.2168 0.2134 0.2714 0.2671 RANDOM 60.804
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] -1.52 -0.76 -1.52 2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.956 r_dihedral_angle_3_deg 15.758 r_dihedral_angle_4_deg 11.234 r_dihedral_angle_1_deg 5.956 r_scangle_it 1.436 r_angle_refined_deg 1.153 r_mcangle_it 0.931 r_angle_other_deg 0.856 r_scbond_it 0.776 r_mcbond_it 0.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.956 r_dihedral_angle_3_deg 15.758 r_dihedral_angle_4_deg 11.234 r_dihedral_angle_1_deg 5.956 r_scangle_it 1.436 r_angle_refined_deg 1.153 r_mcangle_it 0.931 r_angle_other_deg 0.856 r_scbond_it 0.776 r_mcbond_it 0.501 r_chiral_restr 0.056 r_mcbond_other 0.04 r_bond_refined_d 0.009 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 1761 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 19
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction