8PQM | pdb_00008pqm

The DNA-binding domain of L-lactate utilization repressor (LutR-DBD) from Bacillus subtilis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	ITasser

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	Morpheus screen solution: 0.1 M sodium HEPES/MOPS (acid) buffer system (pH 7.5), 37.5% (v/v) 2 methyl 2,4 pentanediol, 37.5% (v/v) PEG 1000, 37.5% (v/v) PEG 3350, 0.03 M NaF, 0.03 M NaBr, 0.03 M NaI Volume ratio (protein:solution) = 1ul : 2ul Plate: EasyXtal 15 well plate (NeXtal Biotechnologies, Holland)

Crystal Properties
Matthews coefficient	Solvent content
1.79	30.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.31	α = 90
b = 38.37	β = 90
c = 66.71	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 PILATUS 6M		2022-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9797	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.46	50	100	0.067	0.073	0.9990000000000001	12.26	6.76		24387

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.46	1.55			3.1189999999999998	3.388	0.319

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.46	33.38	12527	660	99.98	0.20402	0.20221	0.2086	0.23735	0.239	RANDOM	40.221

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]
0.77			-0.95		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.925
r_dihedral_angle_2_deg	13.993
r_long_range_B_refined	13.299
r_long_range_B_other	13.038
r_scangle_other	7.679
r_mcangle_it	7.112
r_mcangle_other	7.111
r_dihedral_angle_1_deg	6.272
r_scbond_other	5.15
r_scbond_it	5.147
r_mcbond_it	4.382
r_mcbond_other	4.37
r_angle_refined_deg	1.572
r_angle_other_deg	0.556
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	593
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
MOLREP	phasing