5IDI

Structure of beta glucosidase 1A from Thermotoga neapolitana, mutant E349A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CBV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5288Protein at 12 mg/ml in 20 mM citrate phosphate buffer, pH 5.6. Hanging drops consisting of 1 microlitre of protein solution and 2 microlitres of reservoir solution (18-23% w/v PEG 6000, 0.2 M sodium chloride, 0.1 M sodium acetate, pH 5.0) equilibrated against 1 ml of reservoir solution. Rod-shaped crystals of approximate dimensions 0.3 x 0.2 x 0.3 mm grew after 8-10 days.
Crystal Properties
Matthews coefficientSolvent content
2.4750.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.277α = 90
b = 98.726β = 90
c = 154.756γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2011-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.0402MAX III911-2

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
11.930.199.10.08412.6581717
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)
11.91.9385.41.1721.9

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 REPLACEMENTTHROUGHOUT2CBV1.93077455409698.850.170820.168570.2147RANDOM27.434
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]
1.04-0.42-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.831
r_dihedral_angle_4_deg21.985
r_dihedral_angle_3_deg14.176
r_dihedral_angle_1_deg6.696
r_long_range_B_refined4.992
r_long_range_B_other4.947
r_scangle_other3.433
r_angle_refined_deg2.24
r_scbond_it2.202
r_scbond_other2.202
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.831
r_dihedral_angle_4_deg21.985
r_dihedral_angle_3_deg14.176
r_dihedral_angle_1_deg6.696
r_long_range_B_refined4.992
r_long_range_B_other4.947
r_scangle_other3.433
r_angle_refined_deg2.24
r_scbond_it2.202
r_scbond_other2.202
r_mcangle_it1.84
r_mcangle_other1.84
r_mcbond_it1.313
r_mcbond_other1.283
r_angle_other_deg1.191
r_chiral_restr0.155
r_bond_refined_d0.027
r_gen_planes_refined0.014
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms7300
Nucleic Acid Atoms
Solvent Atoms429
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing