9HHU | pdb_00009hhu

Plant membrane receptor IGP1 in complex with cellotriose

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	100 mM Sodium acetate pH 4.6, 200 mM Ammonium sulfate, 30 % w/v PEG 2000

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.775	α = 90
b = 83.775	β = 90
c = 198.935	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		2023-03-27	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	2.16	48.95	100	0.12	0.138	0.069	0.998	10	7.8		42267			45.37

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)
	2.16	2.23	100		2.067	2.474	1.336	0.316	1	6.5

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	2.16	48.95	42194	2076	99.983	0.171	0.169	0.1748	0.2105	0.2128	51.647

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]
0.537	0.269		0.537		-1.743

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.677
r_dihedral_angle_3_deg	14.162
r_dihedral_angle_2_deg	8.887
r_lrange_other	8.629
r_lrange_it	8.626
r_scangle_it	8.318
r_scangle_other	8.28
r_dihedral_angle_1_deg	7.63
r_scbond_it	6.152
r_scbond_other	6.112
r_mcangle_it	5.35
r_mcangle_other	5.349
r_dihedral_angle_other_1_deg	4.439
r_mcbond_it	3.807
r_mcbond_other	3.806
r_angle_refined_deg	2.289
r_angle_other_deg	0.774
r_nbd_other	0.231
r_nbd_refined	0.218
r_symmetry_nbd_other	0.21
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.145
r_symmetry_nbd_refined	0.141
r_chiral_restr	0.104
r_symmetry_nbtor_other	0.096
r_symmetry_xyhbond_nbd_refined	0.081
r_metal_ion_refined	0.072
r_symmetry_xyhbond_nbd_other	0.025
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4448
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	312

Software

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