1NO3

REFINED STRUCTURE OF SOYBEAN LIPOXYGENASE-3 WITH 4-NITROCATECHOL AT 2.15 ANGSTROM RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BYTPDB ENTRY 1BYT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.329520% PEG 8000, citrate-phosphate buffer 0.05M, tris.HCl, 0.2% sodium azide, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3346.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.905α = 90
b = 137.531β = 95.48
c = 61.88γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295IMAGE PLATERIGAKU RAXIS IVFocusing mirrors1997-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.15400.9880.07913.72509785034334.02
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)
12.152.230.9930.3462.1425046

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1BYT2.15104998947446254399.080.18870.18870.18630.2326RANDOM26.82
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]
0.910.970.63-1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.451
r_scangle_it4.163
r_scbond_it2.902
r_angle_refined_deg1.979
r_mcangle_it1.652
r_mcbond_it0.929
r_symmetry_hbond_refined0.298
r_xyhbond_nbd_refined0.202
r_nbd_refined0.161
r_symmetry_vdw_refined0.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.451
r_scangle_it4.163
r_scbond_it2.902
r_angle_refined_deg1.979
r_mcangle_it1.652
r_mcbond_it0.929
r_symmetry_hbond_refined0.298
r_xyhbond_nbd_refined0.202
r_nbd_refined0.161
r_symmetry_vdw_refined0.148
r_chiral_restr0.13
r_bond_refined_d0.016
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6799
Nucleic Acid Atoms
Solvent Atoms494
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CCP4phasing