9VV9 | pdb_00009vv9

Crystal structure of the first StART-like domain of Arabidopsis C2 and GRAM domain-containing (C2GR) protein in complex with beta-sitosterol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6GQF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1 M imidazole & MES (pH 6.5), 12.5% MPD, and 17% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.894	α = 90
b = 73.894	β = 90
c = 142.607	γ = 120

Symmetry
Space Group	P 31 1 2

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 PILATUS3 R 200K-A		2022-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.79	50	94.8	0.1	0.999	18.4	6.9		10743

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9			1.1	0.681

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	2.794	21.557	10739	561	94.859	0.224	0.2227	0.2248	0.2475	0.2486	75.627

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]
-0.611	-0.305		-0.611		1.982

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	21.361
r_lrange_other	21.361
r_dihedral_angle_6_deg	16.192
r_scangle_it	14.271
r_scangle_other	14.267
r_mcangle_it	13.847
r_mcangle_other	13.843
r_dihedral_angle_3_deg	12.084
r_scbond_it	9.464
r_scbond_other	9.464
r_mcbond_it	9.402
r_mcbond_other	9.391
r_dihedral_angle_1_deg	7.596
r_dihedral_angle_2_deg	3.638
r_angle_refined_deg	1.652
r_angle_other_deg	0.577
r_symmetry_nbd_other	0.212
r_nbd_other	0.196
r_nbd_refined	0.187
r_nbtor_refined	0.183
r_symmetry_nbtor_other	0.087
r_symmetry_nbd_refined	0.081
r_chiral_restr	0.072
r_xyhbond_nbd_refined	0.064
r_symmetry_xyhbond_nbd_refined	0.031
r_ext_dist_refined_b	0.02
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2767
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing