2QIM

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherCrystal structure of LlPR-10.2F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52921.2 M sodium citrate, 0.1 M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
3.1360.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.822α = 90
b = 73.822β = 90
c = 67.212γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHmirrors2005-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8030EMBL/DESY, HAMBURGX13

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
11.35151000.04256.79.74568545644-1
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)
11.351.41000.672.510.1

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTLlPR-10.2F1.35154568544481116399.990.148430.147250.19438RANDOM19.218
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]
-0.37-0.18-0.370.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.155
r_sphericity_free24.169
r_scangle_it11.702
r_dihedral_angle_3_deg11.498
r_sphericity_bonded11.39
r_scbond_it9.167
r_mcangle_it6.031
r_dihedral_angle_1_deg5.844
r_mcbond_it5.053
r_rigid_bond_restr4.477
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.155
r_sphericity_free24.169
r_scangle_it11.702
r_dihedral_angle_3_deg11.498
r_sphericity_bonded11.39
r_scbond_it9.167
r_mcangle_it6.031
r_dihedral_angle_1_deg5.844
r_mcbond_it5.053
r_rigid_bond_restr4.477
r_mcbond_other3.893
r_angle_refined_deg2.043
r_angle_other_deg0.96
r_dihedral_angle_4_deg0.408
r_nbd_refined0.215
r_nbtor_refined0.194
r_xyhbond_nbd_refined0.192
r_nbd_other0.19
r_metal_ion_refined0.152
r_symmetry_vdw_other0.151
r_symmetry_hbond_refined0.146
r_chiral_restr0.112
r_symmetry_vdw_refined0.102
r_nbtor_other0.089
r_bond_refined_d0.02
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1184
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing