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Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis at pH 4.2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.2 291 0.1 M sodium phosphate, 2 M ammonium sulfate, pH 4.2, vapor diffusion, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.8 56.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.827 α = 90 b = 136.827 β = 90 c = 57.108 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 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 2.35 40 98.3 0.092 15.9 7.6 25344
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 2.35 2.43 97.4 0.488 7.6 2478
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 2.35 20 25014 1283 96.19 0.2275 0.225 0.2192 0.275 0.2669 RANDOM 49.4395
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] -0.03 -0.01 -0.03 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.816 r_dihedral_angle_4_deg 15.875 r_dihedral_angle_3_deg 15.528 r_dihedral_angle_1_deg 6.317 r_scangle_it 3.591 r_scbond_it 2.131 r_mcangle_it 1.395 r_angle_refined_deg 1.365 r_mcbond_it 0.727 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.816 r_dihedral_angle_4_deg 15.875 r_dihedral_angle_3_deg 15.528 r_dihedral_angle_1_deg 6.317 r_scangle_it 3.591 r_scbond_it 2.131 r_mcangle_it 1.395 r_angle_refined_deg 1.365 r_mcbond_it 0.727 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3522 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 40
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction