8B2R

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikF with a rice (Oryza sativa) RGA5 HMA domain mutant.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7B1I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5291.150.1 M BIS-TRIS pH 5.5 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
1.9336.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.906α = 90
b = 57.896β = 90
c = 76.657γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.2246.24299.40.069114.511.542985
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.221.241.7190.324

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7B1I1.2246.24242836212599.3970.1530.15020.203716.484
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]
-1.9550.5821.373
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.16
r_dihedral_angle_3_deg13.677
r_dihedral_angle_2_deg9.678
r_dihedral_angle_1_deg6.728
r_rigid_bond_restr5.437
r_lrange_it4.218
r_lrange_other4.129
r_scangle_it3.984
r_scangle_other3.982
r_scbond_it3.575
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.16
r_dihedral_angle_3_deg13.677
r_dihedral_angle_2_deg9.678
r_dihedral_angle_1_deg6.728
r_rigid_bond_restr5.437
r_lrange_it4.218
r_lrange_other4.129
r_scangle_it3.984
r_scangle_other3.982
r_scbond_it3.575
r_scbond_other3.573
r_mcangle_it2.644
r_mcangle_other2.642
r_mcbond_it2.207
r_mcbond_other2.207
r_angle_refined_deg1.808
r_angle_other_deg0.614
r_symmetry_xyhbond_nbd_refined0.328
r_xyhbond_nbd_refined0.289
r_nbd_refined0.286
r_symmetry_nbd_refined0.275
r_nbd_other0.236
r_symmetry_xyhbond_nbd_other0.21
r_symmetry_nbd_other0.206
r_nbtor_refined0.173
r_chiral_restr0.101
r_symmetry_nbtor_other0.088
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1282
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing