3E85

Crystal Structure of Pathogenesis-related Protein LlPR-10.2B from yellow lupine in complex with Diphenylurea


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QIMPDB entry 2QIM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62921.4 M Sodium citrate, 0.1 M citrate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
1.8633.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.362α = 90
b = 73.256β = 90
c = 99.956γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2005-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.81EMBL/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
11.954099.560.07520.85.79529-337.9
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)
11.952.0296.80.3983.85.4

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 2QIM1.9515863186099.540.193230.187880.2465RANDOM30.611
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]
-1.66-1.343
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.895
r_dihedral_angle_3_deg16.875
r_scangle_it6.456
r_dihedral_angle_1_deg6.214
r_dihedral_angle_4_deg5.89
r_scbond_it4.229
r_angle_refined_deg1.878
r_mcangle_it1.85
r_mcbond_it1.044
r_angle_other_deg0.941
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.895
r_dihedral_angle_3_deg16.875
r_scangle_it6.456
r_dihedral_angle_1_deg6.214
r_dihedral_angle_4_deg5.89
r_scbond_it4.229
r_angle_refined_deg1.878
r_mcangle_it1.85
r_mcbond_it1.044
r_angle_other_deg0.941
r_nbd_refined0.244
r_mcbond_other0.241
r_symmetry_hbond_refined0.217
r_nbd_other0.211
r_nbtor_refined0.195
r_metal_ion_refined0.192
r_symmetry_vdw_refined0.157
r_xyhbond_nbd_refined0.152
r_symmetry_vdw_other0.144
r_chiral_restr0.106
r_nbtor_other0.096
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1155
Nucleic Acid Atoms
Solvent Atoms134
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing