8J68

Crystal structure of the LOV1 R60K 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	sodium phosphate monobasic monohydrate, potassium phosphate dibasic at pH 6.9

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.905	α = 90
b = 53.905	β = 90
c = 137.408	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 PILATUS3 2M		2022-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965459	ESRF	MASSIF-1

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	1.845	53.905	84.8	0.999	12.7	6.5		15532

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	1.845	5.005			0.999

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	1.845	38.146	12770	668	70.007	0.173	0.1708	0.2241	34.307

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]
-0.016			-0.016		0.031

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.348
r_dihedral_angle_6_deg	15.046
r_lrange_it	8.973
r_lrange_other	8.942
r_dihedral_angle_2_deg	8.571
r_scangle_it	7.239
r_scangle_other	7.234
r_dihedral_angle_1_deg	6.854
r_scbond_it	4.867
r_mcangle_it	4.825
r_scbond_other	4.825
r_mcangle_other	4.824
r_mcbond_it	3.532
r_mcbond_other	3.53
r_angle_refined_deg	1.592
r_angle_other_deg	0.528
r_symmetry_xyhbond_nbd_refined	0.238
r_nbd_refined	0.236
r_symmetry_nbd_other	0.206
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.174
r_nbd_other	0.151
r_symmetry_nbd_refined	0.126
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.077
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	962
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	31

Software

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