8IL9 | pdb_00008il9

Crystal structure of the LOV1 Q122N mutant of Klebsormidium nitens phototropin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8I11

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289.15	Nickel chloride hexahydrate, Tris pH 8.5, lithium sulfate monohydrate

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.878	α = 90
b = 53.878	β = 90
c = 137.406	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 EIGER2 X 9M		2022-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.918402	ESRF	ID30B

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	2.156	38.098	98.6	0.095	1	21.5	24.4		13135

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	2.156	5.847	98.6		1

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	2.16	38	10780	612	98.462	0.187	0.1845	0.2	0.2224	0.22	45.953

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]
0.416			0.416		-0.831

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.003
r_dihedral_angle_3_deg	16.296
r_lrange_other	10.438
r_lrange_it	10.405
r_scangle_it	9.498
r_scangle_other	9.491
r_dihedral_angle_2_deg	9.226
r_dihedral_angle_1_deg	7.113
r_scbond_it	6.449
r_scbond_other	6.448
r_mcangle_it	6.422
r_mcangle_other	6.422
r_mcbond_it	4.877
r_mcbond_other	4.811
r_angle_refined_deg	1.684
r_angle_other_deg	0.561
r_nbd_refined	0.23
r_symmetry_nbd_refined	0.21
r_symmetry_nbd_other	0.203
r_symmetry_xyhbond_nbd_refined	0.192
r_nbtor_refined	0.189
r_xyhbond_nbd_refined	0.165
r_nbd_other	0.161
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.082
r_xyhbond_nbd_other	0.024
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	896
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	31

Software

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