8IYN

Crystal structure of LOV1 D33N mutant 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	8I11

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289.15	sodium phoshate monobasic monohydrate , potassium phosphate dibasic , pH 8.2

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.451	α = 90
b = 53.451	β = 90
c = 138.514	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		2022-09-29	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)	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	2.08	49.867	95.1	0.997	10.8	20		12100

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	2.081	6.622			0.997

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	2.081	49.867	9452	476	74.128	0.172	0.1699	0.211	31.488

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]
-0.18			-0.18		0.361

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.775
r_dihedral_angle_6_deg	14.87
r_dihedral_angle_2_deg	10.689
r_lrange_it	8.665
r_lrange_other	8.463
r_dihedral_angle_1_deg	7.376
r_scangle_it	5.758
r_scangle_other	5.754
r_mcangle_other	4.747
r_mcangle_it	4.744
r_scbond_other	3.626
r_scbond_it	3.618
r_mcbond_it	2.913
r_mcbond_other	2.912
r_angle_refined_deg	1.452
r_angle_other_deg	0.462
r_xyhbond_nbd_refined	0.257
r_nbd_refined	0.24
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.188
r_symmetry_xyhbond_nbd_refined	0.174
r_symmetry_nbd_refined	0.162
r_nbd_other	0.155
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.06
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	916
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	31

Software

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