4XPS

Crystal structure of the mutant D365A of Pedobacter saltans GH31 alpha-galactosidase complexed with p-nitrophenyl-alpha-galactopyranoside


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829320% PEG MME 2000, 100 mM HEPES-NaOH, soaked with 20 mM pNP-alpha-galactopyranoside
Crystal Properties
Matthews coefficientSolvent content
2.1943.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.954α = 90
b = 111.954β = 90
c = 113.991γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702014-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.15099.30.09124.19.742959
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.181000.5763.48.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4XPO2.15039532206697.050.199630.197070.24906RANDOM32.018
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.346
r_dihedral_angle_4_deg16.607
r_dihedral_angle_3_deg15.185
r_dihedral_angle_1_deg6.622
r_long_range_B_refined4.978
r_long_range_B_other4.947
r_scangle_other3.306
r_mcangle_it2.558
r_mcangle_other2.558
r_scbond_it2.156
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.346
r_dihedral_angle_4_deg16.607
r_dihedral_angle_3_deg15.185
r_dihedral_angle_1_deg6.622
r_long_range_B_refined4.978
r_long_range_B_other4.947
r_scangle_other3.306
r_mcangle_it2.558
r_mcangle_other2.558
r_scbond_it2.156
r_scbond_other2.156
r_mcbond_it1.745
r_mcbond_other1.743
r_angle_refined_deg1.438
r_angle_other_deg0.781
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5332
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing