8I11

Crystal structure of LOV1 domain of phototropin from Klebsormidium nitens

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	289.15	magnesium Sulfate hydrate, HEPES sodium pH 7.0, lithium sulfate monohydrate

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.868	α = 90
b = 53.868	β = 90
c = 137.014	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 EIGER X 9M		2022-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.88560	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.85	42.34	99.7	0.99	17.7	6.8		17804

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.855	5			0.79

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.855	42.34	17802	904	99.619	0.195	0.1933	0.2208	39.681

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]
-0.067			-0.067		0.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.828
r_dihedral_angle_3_deg	16.785
r_dihedral_angle_6_deg	16.634
r_lrange_other	10.034
r_lrange_it	10.021
r_scangle_it	8.105
r_scangle_other	8.1
r_dihedral_angle_1_deg	6.562
r_mcangle_it	5.989
r_mcangle_other	5.985
r_scbond_other	5.375
r_scbond_it	5.369
r_mcbond_it	3.877
r_mcbond_other	3.877
r_angle_refined_deg	1.661
r_angle_other_deg	0.907
r_symmetry_nbd_refined	0.257
r_nbd_other	0.248
r_nbd_refined	0.234
r_symmetry_nbd_other	0.223
r_nbtor_refined	0.186
r_symmetry_xyhbond_nbd_refined	0.171
r_xyhbond_nbd_refined	0.145
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.084
r_gen_planes_other	0.013
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	979
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing