5LDR

Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain in complex with galactose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529324% PEG 2000 0.2M ammonium acetate 0.1M Bis-Tris pH 5.0
Crystal Properties
Matthew coefficientSolvent content
2.6253.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.26α = 90
b = 107.58β = 90
c = 201.55γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6Mmirrors2013-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X131.017EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
13.155096.70.1760.9837.773.6529579
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.153.2594.40.8480.6431.633.64

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 REPLACEMENTTHROUGHOUT5EUV3.1546.2728097148096.680.188060.183940.26658RANDOM62.444
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]
-3.616.47-2.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.192
r_dihedral_angle_4_deg19.726
r_dihedral_angle_3_deg19.29
r_long_range_B_other12.346
r_long_range_B_refined12.346
r_dihedral_angle_1_deg9.226
r_mcangle_other8.215
r_mcangle_it8.215
r_scangle_other7.996
r_mcbond_it5.177
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.192
r_dihedral_angle_4_deg19.726
r_dihedral_angle_3_deg19.29
r_long_range_B_other12.346
r_long_range_B_refined12.346
r_dihedral_angle_1_deg9.226
r_mcangle_other8.215
r_mcangle_it8.215
r_scangle_other7.996
r_mcbond_it5.177
r_mcbond_other5.174
r_scbond_it4.962
r_scbond_other4.962
r_angle_refined_deg2.091
r_angle_other_deg1.172
r_chiral_restr0.1
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11527
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms83

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing