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Crystal structure of putative alpha-L-fucosidase (NP_812709.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.60 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 277 0.200M sodium citrate, 20.00% PEG-3350, No Buffer pH 8.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.55 51.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.052 α = 90 b = 81.532 β = 103.55 c = 111.572 γ = 90
Symmetry Space Group C 1 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) 2009-02-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97828,0.97916 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 1.6 28.072 99.7 0.074 0.074 6.547 3 133836 16.908
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 1.6 1.64 100 0.365 0.365 2 2.9 9900
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.6 28.072 133835 6726 99.65 0.14 0.139 0.168 0.2674 RANDOM 28.212
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] 0.24 -1.1 0.35 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.928 r_dihedral_angle_4_deg 15.135 r_dihedral_angle_3_deg 10.606 r_dihedral_angle_1_deg 4.657 r_scangle_it 3.155 r_scbond_it 2.101 r_angle_refined_deg 1.738 r_mcangle_it 1.291 r_angle_other_deg 1.283 r_mcbond_it 0.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.928 r_dihedral_angle_4_deg 15.135 r_dihedral_angle_3_deg 10.606 r_dihedral_angle_1_deg 4.657 r_scangle_it 3.155 r_scbond_it 2.101 r_angle_refined_deg 1.738 r_mcangle_it 1.291 r_angle_other_deg 1.283 r_mcbond_it 0.803 r_mcbond_other 0.266 r_symmetry_hbond_refined 0.237 r_symmetry_vdw_other 0.213 r_nbd_refined 0.211 r_nbd_other 0.197 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.184 r_metal_ion_refined 0.131 r_chiral_restr 0.11 r_nbtor_other 0.093 r_symmetry_vdw_refined 0.078 r_xyhbond_nbd_other 0.046 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6906 Nucleic Acid Atoms Solvent Atoms 1234 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction