6T74 | pdb_00006t74

New antiparallel dimer of aureochrome 1a LOV domain mutants from Phaeodactylum tricornutum

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5A8B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291.15	in 1.1 M sodium malonate, 0.1 M HEPES pH 7.0, 0.5 % Jeffamine ED-2003 under dark conditions

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.746	α = 90
b = 100.746	β = 90
c = 120.57	γ = 90

Symmetry
Space Group	P 41 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 EIGER X 16M		2019-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00	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	1.9	46.52	99.96	0.01232	0.01742	0.01232	1	24.51	2		49476			38.84

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)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.968	100		0.2919	0.4128	0.2919	0.838	0.2919	2.39	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5a8b	1.9	46.52	46990	2486	99.91	0.1538	0.16	0.1748	0.18	RANDOM	44.958

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]
-0.89			-0.89		1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.033
r_dihedral_angle_4_deg	18.595
r_dihedral_angle_3_deg	13.108
r_dihedral_angle_1_deg	6.423
r_angle_refined_deg	1.652
r_angle_other_deg	1.461
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.033
r_dihedral_angle_4_deg	18.595
r_dihedral_angle_3_deg	13.108
r_dihedral_angle_1_deg	6.423
r_angle_refined_deg	1.652
r_angle_other_deg	1.461
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2205
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	131

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	refinement
XDS	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.