4D1J

The structure of the GH35 beta-galactosidase Bgl35A from Cellvibrio japonicas in complex with 1-Deoxygalactonojirimycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3U7VPDB ENTRY 3U7V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
172.8 M SODIUM ACETATE PH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.754.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.257α = 90
b = 116.095β = 90.05
c = 116.113γ = 90.04
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.85097.10.059.82.2466658-3.720.1
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)
11.81.8395.80.571.42.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3U7V1.8116.114431372342697.080.172860.171690.19482RANDOM28.627
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]
1.40.130.64-0.350.21-1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.442
r_dihedral_angle_4_deg20.418
r_dihedral_angle_3_deg13.394
r_dihedral_angle_1_deg6.608
r_scangle_it3.86
r_mcangle_it2.814
r_scbond_it2.537
r_mcbond_it1.952
r_mcbond_other1.952
r_angle_refined_deg1.466
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.442
r_dihedral_angle_4_deg20.418
r_dihedral_angle_3_deg13.394
r_dihedral_angle_1_deg6.608
r_scangle_it3.86
r_mcangle_it2.814
r_scbond_it2.537
r_mcbond_it1.952
r_mcbond_other1.952
r_angle_refined_deg1.466
r_angle_other_deg1.272
r_symmetry_vdw_refined0.308
r_symmetry_vdw_other0.287
r_nbd_refined0.271
r_nbd_other0.183
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.135
r_xyhbond_nbd_other0.135
r_metal_ion_refined0.123
r_symmetry_hbond_refined0.114
r_chiral_restr0.091
r_nbtor_other0.088
r_symmetry_metal_ion_refined0.073
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.007
r_gen_planes_other0.005
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms33387
Nucleic Acid Atoms
Solvent Atoms4011
Heterogen Atoms131

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing