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Crystal structure of a PTS dependent N-acetyl-galactosamine-IIB component (agaV, SPy_0631) from Streptococcus pyogenes at 1.65 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 30.00% polyethylene glycol 6000, 0.1M HEPES pH 7.0, Additive: 0.005 M Mannose, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.14 42.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.139 α = 90 b = 80.696 β = 105.26 c = 47.213 γ = 90
Symmetry Space Group P 1 21 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 2010-03-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.96109,0.97934,0.97920 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.65 28.638 99.3 0.059 11.6 3.7 36409 36409 20.718
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 1.65 1.69 99 0.491 0.491 1.6 3.6 2678
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 1.65 28.638 36401 1816 99.32 0.1602 0.1584 0.1685 0.1939 0.2042 RANDOM 26.7488
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] 0.66 1.16 -0.93 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.235 r_dihedral_angle_3_deg 11.7 r_dihedral_angle_4_deg 9.895 r_scangle_it 6.759 r_dihedral_angle_1_deg 4.944 r_scbond_it 4.522 r_mcangle_it 2.931 r_mcbond_it 1.77 r_angle_refined_deg 1.55 r_angle_other_deg 0.902
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.235 r_dihedral_angle_3_deg 11.7 r_dihedral_angle_4_deg 9.895 r_scangle_it 6.759 r_dihedral_angle_1_deg 4.944 r_scbond_it 4.522 r_mcangle_it 2.931 r_mcbond_it 1.77 r_angle_refined_deg 1.55 r_angle_other_deg 0.902 r_mcbond_other 0.534 r_chiral_restr 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2488 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 31
Software Software Software Name Purpose SHELX phasing REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing