6GSZ

Crystal structure of native alfa-L-rhamnosidase from Aspergillus terreus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293100 mM MOPS pH 7.0, 40% PEG 300, 20 mM calcium acetate
Crystal Properties
Matthews coefficientSolvent content
2.9658.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.26α = 90
b = 106.248β = 90
c = 119.832γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.918BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
11.385098.20.04831.53.923113722.39
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.381.3977.80.4251.12.2

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 DIFFRACTIONSADTHROUGHOUT1.3845.822036351070990.940.13580.134140.16801RANDOM19.386
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]
-0.320.72-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.469
r_sphericity_free26.92
r_dihedral_angle_1_deg14.885
r_dihedral_angle_4_deg13.773
r_dihedral_angle_3_deg11.058
r_sphericity_bonded10.496
r_rigid_bond_restr6.028
r_long_range_B_refined4.032
r_long_range_B_other4.032
r_scangle_other3.566
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.469
r_sphericity_free26.92
r_dihedral_angle_1_deg14.885
r_dihedral_angle_4_deg13.773
r_dihedral_angle_3_deg11.058
r_sphericity_bonded10.496
r_rigid_bond_restr6.028
r_long_range_B_refined4.032
r_long_range_B_other4.032
r_scangle_other3.566
r_scbond_it3.092
r_scbond_other3.091
r_mcangle_other2.216
r_mcangle_it2.206
r_mcbond_it1.834
r_mcbond_other1.805
r_angle_refined_deg1.681
r_angle_other_deg1.355
r_chiral_restr0.095
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.01
r_bond_other_d0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6791
Nucleic Acid Atoms
Solvent Atoms1254
Heterogen Atoms524

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing