5L77

A glycoside hydrolase mutant with an unreacted activity based probe bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VYO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829312 mg/mL protein stock in mixed 1:1 with 1.2 M NaH2PO4/K2HPO4 (1:9 v/v) at 293 K.
Crystal Properties
Matthews coefficientSolvent content
2.3848.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.17α = 90
b = 45.12β = 115.11
c = 82.04γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.2428.8889.80.99813.73.9126454

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 REPLACEMENTTHROUGHOUT3VYO1.2428.88120177627689.590.130840.129330.16028RANDOM18.698
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]
0.281.26-1.490.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.355
r_sphericity_free32.156
r_sphericity_bonded13.297
r_dihedral_angle_3_deg11.838
r_dihedral_angle_4_deg11.594
r_dihedral_angle_1_deg5.798
r_long_range_B_refined4.344
r_long_range_B_other4.344
r_scangle_other3.397
r_scbond_it2.837
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.355
r_sphericity_free32.156
r_sphericity_bonded13.297
r_dihedral_angle_3_deg11.838
r_dihedral_angle_4_deg11.594
r_dihedral_angle_1_deg5.798
r_long_range_B_refined4.344
r_long_range_B_other4.344
r_scangle_other3.397
r_scbond_it2.837
r_scbond_other2.834
r_rigid_bond_restr2.685
r_mcangle_other2.43
r_mcangle_it2.429
r_mcbond_it1.953
r_mcbond_other1.953
r_angle_refined_deg1.734
r_angle_other_deg1.059
r_chiral_restr0.115
r_bond_refined_d0.016
r_gen_planes_refined0.01
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3457
Nucleic Acid Atoms
Solvent Atoms483
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing