7OGU

Plant peptide hormone receptor complex H1C9S1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5IXO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52910.2 M K/Na tartrate 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.1661.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.962α = 90
b = 169.894β = 96.744
c = 143.547γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2020-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000029SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.8749.09599.60.2110.250.1320.9967.56.9101500
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.872.921.6841.9951.0610.546.7

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-VALUE5IXO2.87249.095101472518599.6210.2390.23820.262252.948
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]
8.384-0.06-3.518-4.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.853
r_dihedral_angle_other_1_deg32.195
r_dihedral_angle_4_deg16.905
r_dihedral_angle_3_deg15.797
r_lrange_it7.988
r_lrange_other7.988
r_dihedral_angle_other_3_deg6.178
r_dihedral_angle_1_deg5.725
r_scangle_it4.139
r_scangle_other4.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.853
r_dihedral_angle_other_1_deg32.195
r_dihedral_angle_4_deg16.905
r_dihedral_angle_3_deg15.797
r_lrange_it7.988
r_lrange_other7.988
r_dihedral_angle_other_3_deg6.178
r_dihedral_angle_1_deg5.725
r_scangle_it4.139
r_scangle_other4.139
r_mcangle_it3.788
r_mcangle_other3.788
r_scbond_it2.705
r_scbond_other2.705
r_mcbond_it2.333
r_mcbond_other2.333
r_angle_refined_deg1.308
r_angle_other_deg1.287
r_symmetry_nbd_refined0.225
r_symmetry_xyhbond_nbd_refined0.221
r_nbd_other0.208
r_symmetry_nbd_other0.19
r_nbd_refined0.18
r_ext_dist_refined_d0.17
r_nbtor_refined0.161
r_metal_ion_refined0.152
r_xyhbond_nbd_refined0.126
r_symmetry_nbtor_other0.086
r_ncsr_local_group_70.076
r_ncsr_local_group_140.066
r_xyhbond_nbd_other0.064
r_ncsr_local_group_20.059
r_ncsr_local_group_120.056
r_ncsr_local_group_90.054
r_ncsr_local_group_10.053
r_chiral_restr0.052
r_ncsr_local_group_30.052
r_ncsr_local_group_130.052
r_ncsr_local_group_50.051
r_ncsr_local_group_110.049
r_ncsr_local_group_100.047
r_ncsr_local_group_80.046
r_ncsr_local_group_60.045
r_ncsr_local_group_40.043
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_symmetry_xyhbond_nbd_other0.005
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms23182
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms1147

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
Cootmodel building