9VF8 | pdb_00009vf8

Structure of Meiothermus ruber Mrub_1259 LOV domain (MrLOV)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-D3PRD8-F1	residues 15-119

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Ammonium sulfate 0.1 M Sodium cacodylate 6.5 30 % w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
4.31	71.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.593	α = 90
b = 78.593	β = 90
c = 73.381	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 16M		2023-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17UM	0.97918	SSRF	BL17UM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3.352	44.303	91.1	0.5299	0.5432	0.1174	0.987	5.13	21.69		2991

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.352	3.767	59.4		4.1742	4.2668	0.8687	0.847	1.34	22.9	425

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	3.352	44.303	2991	134	83.292	0.244	0.2422	0.2547	0.2721	0.2655	83.668

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]
-0.749			-0.749		1.499

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	24.524
r_lrange_other	24.513
r_scangle_it	19.433
r_scangle_other	19.419
r_mcangle_it	19.237
r_mcangle_other	19.219
r_mcbond_it	13.027
r_mcbond_other	13.024
r_scbond_it	12.835
r_scbond_other	12.815
r_dihedral_angle_3_deg	9.984
r_dihedral_angle_6_deg	6.739
r_dihedral_angle_1_deg	3.352
r_dihedral_angle_2_deg	1.338
r_angle_refined_deg	1.057
r_angle_other_deg	0.315
r_symmetry_nbd_other	0.254
r_symmetry_nbd_refined	0.241
r_nbd_other	0.219
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.185
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.04
r_chiral_restr	0.037
r_bond_refined_d	0.002
r_gen_planes_refined	0.001
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	829
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	31

Software

Software
Software Name	Purpose
XDS	data reduction
STARANISO	data scaling
Aimless	data scaling
REFMAC	refinement
MOLREP	phasing