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Crystal structure of an endo-beta-N-acetylglucosaminidase (BT_3987) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.55 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 1.0M NaCitrate, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.16 42.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.449 α = 90 b = 74.449 β = 90 c = 133.913 γ = 120
Symmetry Space Group P 31 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 ADSC QUANTUM 315 2010-10-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9537,0.9795,0.9793 ALS 8.2.2
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 1.55 29.712 99.3 0.051 17.76 62783 -3 16.663
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 1.55 1.61 94.1 0.357 2.5
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 1.55 29.712 62730 3178 99.52 0.1375 0.1361 0.1483 0.1636 0.1786 RANDOM 23.5834
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] 0.34 0.17 0.34 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.445 r_dihedral_angle_4_deg 16.035 r_dihedral_angle_3_deg 11.471 r_dihedral_angle_1_deg 6.078 r_scangle_it 5.558 r_scbond_it 3.66 r_mcangle_it 2.436 r_mcbond_it 1.523 r_angle_refined_deg 1.511 r_angle_other_deg 0.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.445 r_dihedral_angle_4_deg 16.035 r_dihedral_angle_3_deg 11.471 r_dihedral_angle_1_deg 6.078 r_scangle_it 5.558 r_scbond_it 3.66 r_mcangle_it 2.436 r_mcbond_it 1.523 r_angle_refined_deg 1.511 r_angle_other_deg 0.927 r_mcbond_other 0.45 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3325 Nucleic Acid Atoms Solvent Atoms 612 Heterogen Atoms 5
Software Software Software Name Purpose SHELX phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing