9VLI | pdb_00009vli

Crystal structure of Bacillus subtilis DegQ S25L mutant

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
1.74	29.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.715	α = 90
b = 41.92	β = 90
c = 132.602	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	95	CCD	ADSC QUANTUM 210		2017-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.03912	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.6	100	99.9	0.085	19.8	13.9		21288

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66	100		0.543	6.4

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	1.6	27.144	21147	1094	99.408	0.212	0.21	0.2182	0.2545	0.2665	15.533

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]
-0.041			0.007		0.034

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.635
r_dihedral_angle_6_deg	11.661
r_dihedral_angle_1_deg	3.604
r_lrange_it	3.555
r_lrange_other	3.375
r_dihedral_angle_2_deg	2.832
r_mcangle_it	1.4
r_mcangle_other	1.399
r_scangle_it	1.277
r_scangle_other	1.276
r_angle_refined_deg	0.905
r_mcbond_it	0.763
r_mcbond_other	0.763
r_scbond_it	0.717
r_scbond_other	0.716
r_angle_other_deg	0.359
r_nbd_other	0.224
r_nbd_refined	0.216
r_symmetry_nbd_refined	0.205
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.134
r_xyhbond_nbd_refined	0.106
r_symmetry_nbtor_other	0.066
r_chiral_restr	0.043
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1521
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
Arcimboldo	phasing