3VDB

E. coli (lacZ) beta-galactosidase (N460T) in complex with galactonolactone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JZ5PDB ENTRY 1JZ5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.528810% PEG8000, 100 mM Bis-Tris, pH 6.5, 200 mM magnesium chloride, 100 mM sodium chloride, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.5852.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.443α = 90
b = 161.643β = 90
c = 202.155γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11587ALS8.3.1

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
12.05204.1281.10.043132.124966124966118.114
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)
12.052.1652.30.0735.51.323130

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1JZ52.0575.0524568524568535641000.157250.157250.156570.20532CONSISTENT WITH PREVIOUS STRUCTURES26.514
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]
-0.230.58-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.724
r_dihedral_angle_4_deg14.157
r_dihedral_angle_3_deg12.833
r_scangle_it6.232
r_dihedral_angle_1_deg6.115
r_scbond_it4.587
r_mcangle_it3.118
r_mcbond_it2.181
r_angle_refined_deg1.056
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.724
r_dihedral_angle_4_deg14.157
r_dihedral_angle_3_deg12.833
r_scangle_it6.232
r_dihedral_angle_1_deg6.115
r_scbond_it4.587
r_mcangle_it3.118
r_mcbond_it2.181
r_angle_refined_deg1.056
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms32624
Nucleic Acid Atoms
Solvent Atoms3458
Heterogen Atoms379

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing