7ODK

Plant peptide hormone receptor H1


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 ammonium sulfate 0.1 M citric acid pH 4.0 30% w/v PEG 1000
Crystal Properties
Matthews coefficientSolvent content
3.5765.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.539α = 99.178
b = 84.001β = 113.727
c = 89.061γ = 108.41
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2019-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000033SLSX06DA

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
11.8347.08497.40.0420.060.0420.99910.33.5158310
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)
11.831.860.590.8340.590.7213.6

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-VALUE5IXO1.8347.08158310801397.3920.2050.20440.216429.287
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]
-0.733-0.079-0.1271.131-1.0750.443
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.24
r_dihedral_angle_other_1_deg34.523
r_dihedral_angle_4_deg13.785
r_dihedral_angle_3_deg13.385
r_dihedral_angle_1_deg4.774
r_lrange_it3.375
r_lrange_other3.363
r_scangle_it1.669
r_scangle_other1.669
r_angle_other_deg1.283
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.24
r_dihedral_angle_other_1_deg34.523
r_dihedral_angle_4_deg13.785
r_dihedral_angle_3_deg13.385
r_dihedral_angle_1_deg4.774
r_lrange_it3.375
r_lrange_other3.363
r_scangle_it1.669
r_scangle_other1.669
r_angle_other_deg1.283
r_scbond_it1.205
r_scbond_other1.205
r_mcangle_it1.201
r_mcangle_other1.201
r_angle_refined_deg1.102
r_mcbond_it0.674
r_mcbond_other0.674
r_symmetry_metal_ion_refined0.418
r_symmetry_nbd_refined0.231
r_nbd_other0.21
r_symmetry_nbd_other0.18
r_nbd_refined0.179
r_nbtor_refined0.156
r_symmetry_xyhbond_nbd_refined0.129
r_xyhbond_nbd_refined0.096
r_symmetry_nbtor_other0.086
r_ext_dist_refined_d0.076
r_chiral_restr0.046
r_ncsr_local_group_10.045
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8798
Nucleic Acid Atoms
Solvent Atoms672
Heterogen Atoms643

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
Cootmodel building
PHASERphasing