1V03

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
17.52.0 M NH4(SO4)2, 0.1 M HEPERS PH 7.5, 50 MM NACL
Crystal Properties
Matthews coefficientSolvent content
5.9879

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 195.49α = 90
b = 195.49β = 90
c = 195.49γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002003-04-15MSINGLE 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
123999.80.0736.87.985811
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)
122.0799.70.3282.27

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 1E1E2141.4281445429499.80.1890.1870.213RANDOM28.89
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_1_deg5.849
r_scangle_it2.57
r_mcangle_it2.332
r_scbond_it1.702
r_angle_refined_deg1.529
r_mcbond_it1.422
r_symmetry_hbond_refined0.253
r_nbd_refined0.243
r_xyhbond_nbd_refined0.205
r_symmetry_vdw_refined0.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.849
r_scangle_it2.57
r_mcangle_it2.332
r_scbond_it1.702
r_angle_refined_deg1.529
r_mcbond_it1.422
r_symmetry_hbond_refined0.253
r_nbd_refined0.243
r_xyhbond_nbd_refined0.205
r_symmetry_vdw_refined0.144
r_chiral_restr0.112
r_bond_refined_d0.017
r_gen_planes_refined0.007
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 Atoms3898
Nucleic Acid Atoms
Solvent Atoms600
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing