9VF7 | pdb_00009vf7

Structure of Meiothermus ruber Mrub_1259 LOV domain with N- and C-terminal alpha helices (MrLOVe)

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 1-142

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Magnesium acetate tetrahydrate 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.294	α = 90
b = 77.023	β = 90
c = 103.905	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 EIGER2 X 16M		2023-12-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17UM	0.97919	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	2.038	47.281	93.5	0.2774	0.2977	0.1069	0.993	6.58	7.58		24125

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)
	2.038	2.23	77.3		1.8989	2.0173	0.6727	0.468	1.44	8.83	1206

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	AF-D3PRD8-F1	2.4	47.281	20778	1031	87.901	0.232	0.2299	0.2328	0.2794	0.2802	28.683

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]
0.809			0.141		-0.951

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	11.472
r_dihedral_angle_3_deg	10.887
r_dihedral_angle_2_deg	6.059
r_dihedral_angle_1_deg	5.197
r_lrange_it	4.986
r_lrange_other	4.986
r_scangle_it	3.128
r_scangle_other	3.128
r_mcangle_it	2.994
r_mcangle_other	2.994
r_scbond_it	1.886
r_scbond_other	1.884
r_mcbond_it	1.793
r_mcbond_other	1.793
r_angle_refined_deg	1.099
r_angle_other_deg	0.391
r_nbd_other	0.223
r_nbd_refined	0.215
r_symmetry_nbd_other	0.215
r_nbtor_refined	0.178
r_symmetry_nbd_refined	0.153
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.118
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.047
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4271
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	124

Software

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