2WXD

A MICROMOLAR O-SULFATED THIOHYDROXIMATE INHIBITOR BOUND TO PLANT MYROSINASE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E4MPDB ENTRY 1E4M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5TRIS-HCL PH 8, 68 % SAT AMMONIUM SULFATE; PROTEIN IN HEPES PH 6.5, 150 MM NACL, 0.02 MM ZNSO4; HANGING DROPS 2 AND 2 UL
Crystal Properties
Matthews coefficientSolvent content
2.5643

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.245α = 90
b = 137.567β = 90
c = 80.723γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.680.8599.70.085.94.639963115.4
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)
11.61.6998.40.381.713.87

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 1E4M1.668.7894531507599.840.143680.142570.16408RANDOM12.436
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_deg33.636
r_dihedral_angle_4_deg13.544
r_dihedral_angle_3_deg11.154
r_scangle_it6.503
r_dihedral_angle_1_deg6.264
r_scbond_it5.507
r_angle_refined_deg2.574
r_mcangle_it2.533
r_angle_other_deg1.662
r_mcbond_it1.516
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.636
r_dihedral_angle_4_deg13.544
r_dihedral_angle_3_deg11.154
r_scangle_it6.503
r_dihedral_angle_1_deg6.264
r_scbond_it5.507
r_angle_refined_deg2.574
r_mcangle_it2.533
r_angle_other_deg1.662
r_mcbond_it1.516
r_mcbond_other0.539
r_nbd_refined0.374
r_symmetry_hbond_refined0.32
r_symmetry_vdw_other0.289
r_symmetry_vdw_refined0.242
r_xyhbond_nbd_refined0.205
r_nbd_other0.202
r_nbtor_refined0.198
r_chiral_restr0.174
r_metal_ion_other0.1
r_nbtor_other0.097
r_xyhbond_nbd_other0.06
r_bond_refined_d0.03
r_gen_planes_refined0.015
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms4007
Nucleic Acid Atoms
Solvent Atoms764
Heterogen Atoms386

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling