2JF6

Structure of inactive mutant of Strictosidine Glucosidase in complex with strictosidine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JF7PDB ENTRY 2JF7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.35 M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE PH 4.6 11% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.694.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 159α = 90
b = 159β = 90
c = 102.9γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
12.822098.40.0620.228.232951-3
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)
12.822.9799.10.117.628

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 2JF72.822030623162199.10.2250.2220.28RANDOM9
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]
0.430.43-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.77
r_dihedral_angle_4_deg22.907
r_dihedral_angle_3_deg22.61
r_dihedral_angle_1_deg6.83
r_scangle_it3.331
r_scbond_it2.186
r_angle_refined_deg1.624
r_mcangle_it0.863
r_mcbond_it0.462
r_nbd_refined0.334
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.77
r_dihedral_angle_4_deg22.907
r_dihedral_angle_3_deg22.61
r_dihedral_angle_1_deg6.83
r_scangle_it3.331
r_scbond_it2.186
r_angle_refined_deg1.624
r_mcangle_it0.863
r_mcbond_it0.462
r_nbd_refined0.334
r_gen_planes_other0.257
r_symmetry_vdw_refined0.238
r_xyhbond_nbd_refined0.202
r_symmetry_hbond_refined0.142
r_chiral_restr0.114
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7607
Nucleic Acid Atoms
Solvent Atoms77
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing