7ODK

Plant peptide hormone receptor H1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5IXO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	291	0.2 M ammonium sulfate 0.1 M citric acid pH 4.0 30% w/v PEG 1000

Crystal Properties
Matthews coefficient	Solvent content
3.57	65.57

Crystal Data

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

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M		2019-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.000033	SLS	X06DA

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.83	47.084	97.4	0.042	0.06	0.042	0.999	10.3	3.5		158310

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)	Redundancy	Number Unique Reflections (All)
1	1.83	1.86			0.59	0.834	0.59	0.721		3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5IXO	1.83	47.08	158310	8013	97.392	0.205	0.2044	0.2164	29.287

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	-0.127	1.131	-1.075	0.443

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.24
r_dihedral_angle_other_1_deg	34.523
r_dihedral_angle_4_deg	13.785
r_dihedral_angle_3_deg	13.385
r_dihedral_angle_1_deg	4.774
r_lrange_it	3.375
r_lrange_other	3.363
r_scangle_it	1.669
r_scangle_other	1.669
r_angle_other_deg	1.283
r_scbond_it	1.205
r_scbond_other	1.205
r_mcangle_it	1.201
r_mcangle_other	1.201
r_angle_refined_deg	1.102
r_mcbond_it	0.674
r_mcbond_other	0.674
r_symmetry_metal_ion_refined	0.418
r_symmetry_nbd_refined	0.231
r_nbd_other	0.21
r_symmetry_nbd_other	0.18
r_nbd_refined	0.179
r_nbtor_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.129
r_xyhbond_nbd_refined	0.096
r_symmetry_nbtor_other	0.086
r_ext_dist_refined_d	0.076
r_chiral_restr	0.046
r_ncsr_local_group_1	0.045
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8798
Nucleic Acid Atoms
Solvent Atoms	672
Heterogen Atoms	643

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
Coot	model building
PHASER	phasing