9VV7 | pdb_00009vv7

Crystal structure of the first StART-like domain of Arabidopsis C2 and GRAM domain-containing (C2GR) protein in apo form

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 NaAc (pH 4.6) and 1.8 M MgSO4

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.847	α = 90
b = 87.847	β = 90
c = 122.94	γ = 120

Symmetry
Space Group	P 65

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 6M		2020-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.987	SSRF	BL19U1

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	2.097	50	100	0.111	0.997	25.52	13.4		31514

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	2.1	2.18			1.489	0.623

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	2.097	47.813	29284	1508	93.033	0.239	0.2376	0.2413	0.2575	0.2571	33.681

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]
0.127			0.127		-0.254

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.704
r_dihedral_angle_3_deg	11.957
r_lrange_it	10.332
r_lrange_other	10.306
r_dihedral_angle_1_deg	7.365
r_scangle_it	6.724
r_scangle_other	6.723
r_mcangle_it	6.549
r_mcangle_other	6.548
r_dihedral_angle_2_deg	5.756
r_scbond_it	4.526
r_scbond_other	4.525
r_mcbond_it	4.362
r_mcbond_other	4.348
r_angle_refined_deg	1.737
r_angle_other_deg	0.583
r_nbd_other	0.339
r_symmetry_nbd_refined	0.314
r_symmetry_xyhbond_nbd_refined	0.199
r_nbd_refined	0.18
r_symmetry_nbd_other	0.18
r_ncsr_local_group_1	0.174
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_ext_dist_refined_b	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2776
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms

Software

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