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Endo-alpha-N-acetylgalactosaminidase from Streptococcus pneumoniae: SeMet structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 29% (w/v) PEG MME 2000, 0.2 M lithium citrate, 0.1 M ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.73 54.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.611 α = 90 b = 158.209 β = 90 c = 112.436 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315 2006-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9795 ALS 8.2.2
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 2.9 112.509 99.4 0.11 0.11 6.13 6.8 83445 71.87
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 2.9 3.06 97.4 0.592 0.592 2.4 6.3 11781
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 SAD THROUGHOUT 2.9 112.509 83381 4164 99.37 0.192 0.19 0.1977 0.235 0.2394 RANDOM 57.319
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] -0.99 0.91 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.55 r_dihedral_angle_4_deg 18.645 r_dihedral_angle_3_deg 16.777 r_dihedral_angle_1_deg 6.587 r_scangle_it 2.069 r_scbond_it 1.313 r_angle_refined_deg 1.225 r_angle_other_deg 0.823 r_mcangle_it 0.625 r_symmetry_hbond_refined 0.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.55 r_dihedral_angle_4_deg 18.645 r_dihedral_angle_3_deg 16.777 r_dihedral_angle_1_deg 6.587 r_scangle_it 2.069 r_scbond_it 1.313 r_angle_refined_deg 1.225 r_angle_other_deg 0.823 r_mcangle_it 0.625 r_symmetry_hbond_refined 0.331 r_mcbond_it 0.286 r_nbd_refined 0.207 r_nbd_other 0.189 r_metal_ion_refined 0.187 r_nbtor_refined 0.186 r_symmetry_vdw_other 0.168 r_xyhbond_nbd_refined 0.136 r_symmetry_vdw_refined 0.125 r_nbtor_other 0.086 r_mcbond_other 0.08 r_chiral_restr 0.071 r_xyhbond_nbd_other 0.022 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21250 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 18
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling SHARP phasing SOLOMON phasing REFMAC refinement PDB_EXTRACT data extraction