9HHX | pdb_00009hhx

Plant membrane receptor IGP1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	C0LGH4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	292.15	0.1 M Sodium acetate trihydrate pH 4.6 0.2 M Ammonium sulfate 30 % PEG 2000

Crystal Properties
Matthews coefficient	Solvent content
3	59.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.365	α = 90
b = 84.365	β = 90
c = 198.32	γ = 120

Symmetry
Space Group	P 61

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 EIGER X 16M		2023-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.033286	SLS	X06SA

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	2.62	49.58	100	0.428	0.475	0.205	0.973	5.9	10.5		24021

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)
	2.62	2.74	100		2.114	2.412	1.147	0.314	1	8.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.62	49.068	23962	1185	99.987	0.186	0.1823	0.1895	0.2564	0.2577	36.261

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]
0.442	0.221		0.442		-1.434

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.309
r_dihedral_angle_6_deg	15.124
r_dihedral_angle_2_deg	12.944
r_dihedral_angle_1_deg	7.748
r_lrange_other	6.817
r_lrange_it	6.804
r_scangle_it	5.973
r_scangle_other	5.838
r_mcangle_it	4
r_mcangle_other	4
r_scbond_it	3.974
r_scbond_other	3.824
r_mcbond_it	2.521
r_mcbond_other	2.517
r_angle_refined_deg	2.335
r_angle_other_deg	0.788
r_symmetry_nbd_other	0.22
r_nbd_other	0.218
r_nbd_refined	0.215
r_nbtor_refined	0.188
r_symmetry_xyhbond_nbd_refined	0.169
r_xyhbond_nbd_refined	0.159
r_symmetry_nbd_refined	0.147
r_symmetry_xyhbond_nbd_other	0.121
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.095
r_metal_ion_refined	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4479
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	264

Software

Software
Software Name	Purpose
REFMAC	refinement
pointless	data scaling
Aimless	data scaling
Coot	model building
PHENIX	phasing