4UCF

Crystal structure of Bifidobacterium bifidum beta-galactosidase in complex with alpha-galactose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4UZSPDB ENTRY 4UZS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1629220% (W/V) POLYETHYLENE GLYCOL 3, 350, 0.2 M DIBASIC AMMONIUM TARTRATE AND 4% (W/V) 1-PROPANOL AT 292 K, pH 6
Crystal Properties
Matthews coefficientSolvent content
2.3547.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.72α = 90
b = 101.592β = 105.4
c = 114.625γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2010-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
11.942.8970.113.43.71530592
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)
11.92850.6623.4

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 4UZS1.94110.51145369768897.010.157620.155050.20606RANDOM25.194
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]
2.351.06-1.98-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.179
r_dihedral_angle_4_deg16.933
r_dihedral_angle_3_deg13.759
r_dihedral_angle_1_deg6.58
r_mcangle_it2.577
r_scbond_it2.5
r_mcbond_it1.843
r_mcbond_other1.837
r_angle_refined_deg1.739
r_angle_other_deg0.909
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.179
r_dihedral_angle_4_deg16.933
r_dihedral_angle_3_deg13.759
r_dihedral_angle_1_deg6.58
r_mcangle_it2.577
r_scbond_it2.5
r_mcbond_it1.843
r_mcbond_other1.837
r_angle_refined_deg1.739
r_angle_other_deg0.909
r_chiral_restr0.108
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.006
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_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms16138
Nucleic Acid Atoms
Solvent Atoms2021
Heterogen Atoms95

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing