28WB | pdb_000028wb

Crystal structure of the STRUBBELIG-RECEPTOR FAMILY 6 (SRF6) ectodomain from Arabidopsis thaliana

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	298	25% PEG3350, 0.2M NaCl, 0.1M citrate pH 4.0

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.72	α = 90
b = 76.72	β = 90
c = 86.43	γ = 90

Symmetry
Space Group	P 43 21 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 PILATUS 2M		2018-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.977944	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.5	45.95	99.9	0.174	0.999	13.9	13.6		39355		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.59	99.3		2.58	0.508	1.11	12.9

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.501	45.948	41806	2091	99.926	0.164	0.1621	0.1762	0.195	0.203	RANDOM	18.124

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]
0.77			0.77		-1.539

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.892
r_dihedral_angle_3_deg	11
r_dihedral_angle_2_deg	9.84
r_dihedral_angle_1_deg	6.967
r_lrange_it	6.022
r_lrange_other	6.022
r_scangle_it	4.495
r_scangle_other	4.493
r_scbond_it	3.018
r_scbond_other	2.995
r_mcangle_it	2.556
r_mcangle_other	2.555
r_mcbond_it	1.815
r_mcbond_other	1.815
r_angle_refined_deg	1.798
r_angle_other_deg	0.632
r_metal_ion_refined	0.326
r_nbd_refined	0.282
r_symmetry_nbd_refined	0.271
r_symmetry_xyhbond_nbd_refined	0.213
r_symmetry_nbd_other	0.19
r_nbd_other	0.189
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.172
r_symmetry_metal_ion_refined	0.101
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1695
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing