9VLH | pdb_00009vlh

Crystal structure of Bacillus subtilis DegQ tetramer

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	15%(v/v) polyethylene glycol 3350, 5 mM magnesium chloride, 0.1 M HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.548	α = 87.443
b = 52.271	β = 89.567
c = 53.098	γ = 89.936

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	PIXEL	DECTRIS PILATUS3 S 2M		2019-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.00	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.3	100	95.4	0.049	0.059	0.032	12.2	3.4		15256

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.349	81.8		0.197	0.235	0.126	4.2	3.4

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	AB INITIO PHASING	THROUGHOUT	2.3	38.1	15256	780	95.344	0.221	0.2196	0.224	0.2542	0.2604	43.86

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]
-0.238	-1.156	-0.815	-0.471	-0.558	0.641

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.814
r_dihedral_angle_6_deg	15.059
r_lrange_it	10.641
r_lrange_other	10.639
r_dihedral_angle_2_deg	7.479
r_scangle_it	6.937
r_scangle_other	6.935
r_mcangle_it	6.029
r_mcangle_other	6.028
r_scbond_it	4.087
r_scbond_other	4.085
r_dihedral_angle_1_deg	3.86
r_mcbond_it	3.621
r_mcbond_other	3.62
r_angle_refined_deg	1.473
r_angle_other_deg	0.493
r_nbd_refined	0.233
r_symmetry_xyhbond_nbd_refined	0.231
r_nbd_other	0.21
r_symmetry_nbd_refined	0.202
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.168
r_symmetry_xyhbond_nbd_other	0.077
r_symmetry_nbtor_other	0.07
r_chiral_restr	0.064
r_xyhbond_nbd_other	0.019
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2743
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
Arcimboldo	phasing