7PGY | pdb_00007pgy

Structure of light-adapted AsLOV2 wild type

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V0U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.8	298	0.1 M sodium acetate pH 4.6-5.0, 6-8% (w/v) PEG 4000, 30% (v/v) glycerol

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.61	α = 90
b = 56.01	β = 90
c = 66.52	γ = 90

Symmetry
Space Group	P 21 21 21

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 6M		2020-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	1.09	42.845	99.2	0.999	12	7		55866

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	1.09	1.16	98		0.45		6.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	2v0u	1.09	42.845	55866	2100	99.217	0.124	0.1226	0.13	0.1612	0.17	16.033

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]
-0.553			2.004		-1.451

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.19
r_dihedral_angle_4_deg	17.137
r_dihedral_angle_3_deg	12.813
r_dihedral_angle_1_deg	7.121
r_lrange_it	3.214
r_rigid_bond_restr	3.023
r_lrange_other	3.002
r_scangle_it	2.687
r_scangle_other	2.687
r_scbond_other	2.535
r_scbond_it	2.531
r_mcangle_it	1.838
r_mcangle_other	1.837
r_angle_refined_deg	1.821
r_mcbond_it	1.599
r_mcbond_other	1.499
r_angle_other_deg	1.447
r_nbd_refined	0.29
r_symmetry_nbd_refined	0.241
r_symmetry_xyhbond_nbd_refined	0.231
r_nbtor_refined	0.199
r_nbd_other	0.199
r_symmetry_nbd_other	0.197
r_xyhbond_nbd_refined	0.182
r_xyhbond_nbd_other	0.108
r_chiral_restr	0.105
r_symmetry_xyhbond_nbd_other	0.103
r_symmetry_nbtor_other	0.083
r_symmetry_metal_ion_refined	0.073
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1186
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	89

Software

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