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Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with 2'-deoxyguanosine
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 2.72 54.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.352 α = 90 b = 135.352 β = 90 c = 56.801 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 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 2.95 50 99.7 0.127 7.8 10 6857
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 2.95 3.06 98.3 0.51 8.5 651
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 2.95 44.3 6782 321 98.83 0.2308 0.2271 0.2216 0.3095 0.2969 RANDOM 62.8993
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] -0.07 -0.04 -0.07 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.762 r_dihedral_angle_3_deg 17.561 r_dihedral_angle_4_deg 15.441 r_dihedral_angle_1_deg 6.802 r_scangle_it 1.884 r_angle_refined_deg 1.302 r_mcangle_it 1.29 r_scbond_it 1.072 r_mcbond_it 0.761 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.762 r_dihedral_angle_3_deg 17.561 r_dihedral_angle_4_deg 15.441 r_dihedral_angle_1_deg 6.802 r_scangle_it 1.884 r_angle_refined_deg 1.302 r_mcangle_it 1.29 r_scbond_it 1.072 r_mcbond_it 0.761 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1755 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 20
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing