5G0M

beta-glucuronidase with an activity-based probe (N-acyl cyclophellitol aziridine) bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VO0PDB ENTRY 3VO0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.62930.7 UL 4.5 MG/ML PROTEIN STOCK IS MIXED WITH 0.5 UL PRECIPITANT COMPOSED OF 1 M NAH2PO4:K2HPO4 = 0.5:9.5 (V/V) AT 20 DEGREE., pH 8.6
Crystal Properties
Matthews coefficientSolvent content
2.448.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.74α = 90
b = 44.81β = 115.5
c = 83.27γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS2014-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
11.866.71980.0713.64.1458562.1
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)
11.81.85980.542.12.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3VO01.866.7143578227897.660.184120.18260.21319RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.713
r_dihedral_angle_4_deg14.712
r_dihedral_angle_3_deg13.558
r_dihedral_angle_1_deg6.331
r_long_range_B_other4.87
r_long_range_B_refined4.86
r_scangle_other3.441
r_mcangle_it2.385
r_mcangle_other2.385
r_scbond_it2.226
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.713
r_dihedral_angle_4_deg14.712
r_dihedral_angle_3_deg13.558
r_dihedral_angle_1_deg6.331
r_long_range_B_other4.87
r_long_range_B_refined4.86
r_scangle_other3.441
r_mcangle_it2.385
r_mcangle_other2.385
r_scbond_it2.226
r_scbond_other2.213
r_angle_refined_deg1.812
r_mcbond_it1.583
r_mcbond_other1.579
r_angle_other_deg1.066
r_chiral_restr0.112
r_bond_refined_d0.018
r_gen_planes_refined0.009
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 Atoms3430
Nucleic Acid Atoms
Solvent Atoms244
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing