3NMV

Crystal structure of pyrabactin-bound abscisic acid receptor PYL2 mutant A93F in complex with type 2C protein phosphatase ABI2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NMTPDB entry 3NMT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1M HEPES, 10% PEG 8000, 10% sucrose, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6566.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.129α = 90
b = 97.587β = 90
c = 134.505γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.00APS21-ID-D

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
12.13098.20.132.414.74474522

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-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3NMT2.129.641807347199.880.195530.195530.193410.22281RANDOM38.284
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]
-2.615.53-2.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.071
r_dihedral_angle_4_deg20.842
r_sphericity_free19.215
r_dihedral_angle_3_deg16.007
r_sphericity_bonded11.758
r_scangle_it7.111
r_dihedral_angle_1_deg5.754
r_scbond_it4.736
r_mcangle_it3.497
r_rigid_bond_restr2.559
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.071
r_dihedral_angle_4_deg20.842
r_sphericity_free19.215
r_dihedral_angle_3_deg16.007
r_sphericity_bonded11.758
r_scangle_it7.111
r_dihedral_angle_1_deg5.754
r_scbond_it4.736
r_mcangle_it3.497
r_rigid_bond_restr2.559
r_mcbond_it2.08
r_angle_refined_deg1.95
r_angle_other_deg1.07
r_mcbond_other0.753
r_chiral_restr0.133
r_bond_refined_d0.026
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3574
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms25

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling