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Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in space group P212121 at pH 5.6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 291 0.1 M sodium citrate, 2 M ammonium sulfate, 0.2 M sodium potassium tartrate, pH 5.6, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.76 55.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.788 α = 90 b = 135.976 β = 90 c = 236.613 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 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 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 1.61 50 98.8 0.048 12.5 1.8 235074
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 1.61 1.67 93.4 0.187 1.8 22046
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 1.61 20 234488 11788 98.71 0.1674 0.1662 0.1656 0.1896 0.1895 RANDOM 22.806
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] 1.04 -0.82 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.895 r_dihedral_angle_4_deg 17.478 r_dihedral_angle_3_deg 13.169 r_dihedral_angle_1_deg 5.797 r_scangle_it 4.973 r_scbond_it 2.931 r_mcangle_it 1.872 r_angle_refined_deg 1.572 r_mcbond_it 1.037 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.895 r_dihedral_angle_4_deg 17.478 r_dihedral_angle_3_deg 13.169 r_dihedral_angle_1_deg 5.797 r_scangle_it 4.973 r_scbond_it 2.931 r_mcangle_it 1.872 r_angle_refined_deg 1.572 r_mcbond_it 1.037 r_chiral_restr 0.11 r_bond_refined_d 0.015 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10956 Nucleic Acid Atoms Solvent Atoms 964 Heterogen Atoms 138
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling