3GZA

Crystal structure of putative alpha-L-fucosidase (NP_812709.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.60 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.22770.200M sodium citrate, 20.00% PEG-3350, No Buffer pH 8.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
2.5551.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.052α = 90
b = 81.532β = 103.55
c = 111.572γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2009-02-18MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837,0.97828,0.97916SSRLBL11-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.628.07299.70.0740.0746.547313383616.908
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)RedundancyNumber Unique Reflections (All)
11.61.641000.3650.36522.99900

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.628.072133835672699.650.140.1390.168RANDOM28.212
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]
0.24-1.10.35-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.928
r_dihedral_angle_4_deg15.135
r_dihedral_angle_3_deg10.606
r_dihedral_angle_1_deg4.657
r_scangle_it3.155
r_scbond_it2.101
r_angle_refined_deg1.738
r_mcangle_it1.291
r_angle_other_deg1.283
r_mcbond_it0.803
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.928
r_dihedral_angle_4_deg15.135
r_dihedral_angle_3_deg10.606
r_dihedral_angle_1_deg4.657
r_scangle_it3.155
r_scbond_it2.101
r_angle_refined_deg1.738
r_mcangle_it1.291
r_angle_other_deg1.283
r_mcbond_it0.803
r_mcbond_other0.266
r_symmetry_hbond_refined0.237
r_symmetry_vdw_other0.213
r_nbd_refined0.211
r_nbd_other0.197
r_nbtor_refined0.185
r_xyhbond_nbd_refined0.184
r_metal_ion_refined0.131
r_chiral_restr0.11
r_nbtor_other0.093
r_symmetry_vdw_refined0.078
r_xyhbond_nbd_other0.046
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6906
Nucleic Acid Atoms
Solvent Atoms1234
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SOLVEphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction