4A3Y

Crystal structure of Raucaffricine glucosidase from ajmaline biosynthesis pathway


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.01 TO 0.3 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH 4.5 TO 5.0, 9 TO 12% (W/V) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.957

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.774α = 90
b = 127.329β = 90
c = 215.837γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR555 FLAT PANELMIRROR2006-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
12.152099.30.1224.615.376299232
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)
12.152.398.80.694.415

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 2JF72.1519.9975240105499.260.165930.165410.20355RANDOM36.186
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]
-0.120.10.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.565
r_dihedral_angle_4_deg20.364
r_dihedral_angle_3_deg14.597
r_dihedral_angle_1_deg6.241
r_scangle_it3.219
r_scbond_it2.52
r_angle_refined_deg1.689
r_mcangle_it1.137
r_mcbond_it0.69
r_chiral_restr0.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.565
r_dihedral_angle_4_deg20.364
r_dihedral_angle_3_deg14.597
r_dihedral_angle_1_deg6.241
r_scangle_it3.219
r_scbond_it2.52
r_angle_refined_deg1.689
r_mcangle_it1.137
r_mcbond_it0.69
r_chiral_restr0.117
r_bond_refined_d0.023
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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 Atoms7510
Nucleic Acid Atoms
Solvent Atoms443
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing