9J42 | pdb_00009j42

Crystal structure of Glucsoe bound glucose tolerant GH1 beta-glucosidase mutant (UnBGl1_C188V)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 9J3W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.22950.056M Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic, pH 8.2
Crystal Properties
Matthews coefficientSolvent content
2.3447.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.11α = 90
b = 66.98β = 90
c = 138.64γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2016-08-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.754096.90.0710.99819.317.0348288
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)
11.751.85930.2870.9536.646.87

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.7538.0445873241596.940.155660.153770.16570.191150.1992RANDOM13.219
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]
-0.47-0.040.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.443
r_dihedral_angle_2_deg7.125
r_dihedral_angle_1_deg6.701
r_long_range_B_refined4.56
r_long_range_B_other4.26
r_scangle_other2.973
r_scbond_it1.949
r_scbond_other1.938
r_mcangle_other1.779
r_mcangle_it1.773
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.443
r_dihedral_angle_2_deg7.125
r_dihedral_angle_1_deg6.701
r_long_range_B_refined4.56
r_long_range_B_other4.26
r_scangle_other2.973
r_scbond_it1.949
r_scbond_other1.938
r_mcangle_other1.779
r_mcangle_it1.773
r_angle_refined_deg1.602
r_mcbond_it1.227
r_mcbond_other1.206
r_angle_other_deg0.543
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms3566
Nucleic Acid Atoms
Solvent Atoms574
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing