1XDF

Crystal structure of pathogenesis-related protein LlPR-10.2A from yellow lupine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IFVPDB entry 1IFV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5292sodium citrate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.7154.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.956α = 90
b = 69.243β = 90
c = 112.918γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHmirrors2000-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X9B0.9800NSLSX9B

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
11.92599.20.05228.34.33083030830-330.8
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)
11.91.9797.80.4122.73.23000

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 1IFV1.9202857928579119396.750.2070.2070.2050.251RANDOM24.01
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]
-13.13-2.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.333
r_scangle_it6.23
r_scbond_it4.423
r_mcangle_it3.013
r_angle_refined_deg1.783
r_mcbond_it1.779
r_angle_other_deg0.926
r_symmetry_vdw_other0.284
r_nbd_other0.251
r_symmetry_hbond_refined0.242
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.333
r_scangle_it6.23
r_scbond_it4.423
r_mcangle_it3.013
r_angle_refined_deg1.783
r_mcbond_it1.779
r_angle_other_deg0.926
r_symmetry_vdw_other0.284
r_nbd_other0.251
r_symmetry_hbond_refined0.242
r_symmetry_vdw_refined0.226
r_nbd_refined0.222
r_xyhbond_nbd_refined0.171
r_chiral_restr0.105
r_metal_ion_refined0.096
r_nbtor_other0.089
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_gen_planes_other0.006
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2346
Nucleic Acid Atoms
Solvent Atoms281
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing