4HHD

2.75 Angstrom resolution crystal structure of the A. thaliana LOV2 domain with an extended N-terminal A' helix (cryo dark structure)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	287	Protein at 21 mg/mL in 20 mM TRIS-HCl pH 7.4, 20 mM NaCl, 15 % glycerol Crystallization: The JCSG+ Suite (D12: 0.04 M Potassium phosphate, 16% (w/v) PEG 8000, 20% (v/v) glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 287K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.382	α = 90
b = 63.382	β = 90
c = 171.318	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	105	CCD	ADSC QUANTUM 315	Bent conical Si-mirror (Rh coated)	2007-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9002	APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.75	30	87.9	0.07	17.5	3.3	8574	8574	-3		66.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.8	86.6		0.585	2.2	3.6	399

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2V0U	2.75	29.72	8128	8128	417	88.18	0.23399	0.23109	0.2894	RANDOM	48.442

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]
-1.75			-1.75		3.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.087
r_dihedral_angle_3_deg	9.903
r_dihedral_angle_4_deg	7.057
r_dihedral_angle_1_deg	2.771
r_scangle_it	1.787
r_angle_refined_deg	1.312
r_scbond_it	1.071
r_angle_other_deg	0.849
r_mcangle_it	0.8
r_mcbond_it	0.421

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.087
r_dihedral_angle_3_deg	9.903
r_dihedral_angle_4_deg	7.057
r_dihedral_angle_1_deg	2.771
r_scangle_it	1.787
r_angle_refined_deg	1.312
r_scbond_it	1.071
r_angle_other_deg	0.849
r_mcangle_it	0.8
r_mcbond_it	0.421
r_chiral_restr	0.077
r_mcbond_other	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2466
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	63

Software

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

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 R01GM133198.