1V02

Crystal structure of the Sorghum bicolor dhurrinase 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E1EPDB ENTRY 1E1E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1716% PEG-MONO-METHYL-ETHER 2000, 0.1 M TRIS PH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.59352

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.05α = 90
b = 101.05β = 90
c = 279.05γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002003-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.93998.60.06884.3291187
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)
11.91.9789.60.3392.12.7

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 1E1E1.8302763711472098.60.1730.1720.21RANDOM31.02
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]
0.890.440.89-1.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.717
r_scangle_it2.349
r_mcangle_it1.854
r_scbond_it1.572
r_angle_refined_deg1.336
r_mcbond_it1.089
r_symmetry_hbond_refined0.311
r_symmetry_vdw_refined0.298
r_xyhbond_nbd_refined0.275
r_nbd_refined0.265
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.717
r_scangle_it2.349
r_mcangle_it1.854
r_scbond_it1.572
r_angle_refined_deg1.336
r_mcbond_it1.089
r_symmetry_hbond_refined0.311
r_symmetry_vdw_refined0.298
r_xyhbond_nbd_refined0.275
r_nbd_refined0.265
r_chiral_restr0.105
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
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 Atoms23259
Nucleic Acid Atoms
Solvent Atoms5068
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing