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Crystal structure of phage related exonuclease (YP_719632.1) from HAEMOPHILUS SOMNUS 129PT at 2.15 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 10.0000% Glycerol, 1.0000M NaCl, 30.0000% PEG-600, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.03 59.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.369 α = 90 b = 113.369 β = 90 c = 42.284 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 325 mm CCD Flat mirror (vertical focusing) 2009-07-08 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97947 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.15 28.341 100 0.129 0.129 12.8 7.4 17252 32.941
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 2.15 2.21 100 0.836 0.836 2.1 7.5 1285
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 MAD THROUGHOUT 2.15 28.341 17249 874 99.99 0.174 0.172 0.1859 0.212 0.2256 RANDOM 18.489
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] -0.13 -0.07 -0.13 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.597 r_dihedral_angle_4_deg 15.013 r_dihedral_angle_3_deg 14.765 r_dihedral_angle_1_deg 5.373 r_scangle_it 3.765 r_scbond_it 2.271 r_angle_refined_deg 1.459 r_mcangle_it 1.445 r_angle_other_deg 0.971 r_mcbond_it 0.753
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.597 r_dihedral_angle_4_deg 15.013 r_dihedral_angle_3_deg 14.765 r_dihedral_angle_1_deg 5.373 r_scangle_it 3.765 r_scbond_it 2.271 r_angle_refined_deg 1.459 r_mcangle_it 1.445 r_angle_other_deg 0.971 r_mcbond_it 0.753 r_mcbond_other 0.167 r_chiral_restr 0.102 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1775 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction