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Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in space group H32 at pH 7.5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 0.1 M HEPES, 1%(v/v) MPD, 2 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.05 40.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.26 α = 90 b = 158.26 β = 90 c = 93.867 γ = 120
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 1.7 30 95.5 0.093 11.5 8 47177
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 1.7 1.76 92.6 0.382 7 4538
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 1.7 29.81 46951 2375 95.07 0.17 0.1682 0.2059 0.2162 RANDOM 24.0276
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.358 r_dihedral_angle_4_deg 17.658 r_dihedral_angle_3_deg 13.781 r_dihedral_angle_1_deg 5.816 r_scangle_it 5.046 r_scbond_it 2.956 r_mcangle_it 1.727 r_angle_refined_deg 1.557 r_mcbond_it 0.949 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.358 r_dihedral_angle_4_deg 17.658 r_dihedral_angle_3_deg 13.781 r_dihedral_angle_1_deg 5.816 r_scangle_it 5.046 r_scbond_it 2.956 r_mcangle_it 1.727 r_angle_refined_deg 1.557 r_mcbond_it 0.949 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3522 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 18
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling