9S4V | pdb_00009s4v

AcuB from Bacillus subtilis with AMP and ADP

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	protein (13 mg/mL, with 1 mM AMP) + 5% MPD, 5% ethanol, 100 mM HEPES pH 7.5, cryo: 20% MPD, 5% ethanol, 100 mM HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.7	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.305	α = 90
b = 79.779	β = 90
c = 153.788	γ = 90

Symmetry
Space Group	P 21 2 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 PILATUS3 6M		2024-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.97624	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.64	50	97.4	0.137	0.145	0.063	0.998	10	10		24477		-3	73.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.64	2.77	99.2		2.437	2.602	0.8	0.64	1.1	10.3

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	THROUGHOUT	2.64	48.79	24436	1214	97.417	0.209	0.2067	0.2039	0.2664	0.265	100.062

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]
-4.31			6.001		-1.691

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.598
r_dihedral_angle_6_deg	13.159
r_lrange_it	11.391
r_lrange_other	11.39
r_scangle_it	7.915
r_scangle_other	7.914
r_mcangle_it	7.499
r_mcangle_other	7.498
r_dihedral_angle_2_deg	7.289
r_dihedral_angle_1_deg	6.884
r_scbond_it	4.859
r_scbond_other	4.859
r_mcbond_it	4.661
r_mcbond_other	4.66
r_angle_refined_deg	1.359
r_angle_other_deg	0.461
r_nbd_refined	0.206
r_symmetry_nbd_other	0.193
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.159
r_nbd_other	0.152
r_ncsr_local_group_1	0.137
r_symmetry_nbd_refined	0.126
r_ncsr_local_group_2	0.121
r_dihedral_angle_other_2_deg	0.119
r_ncsr_local_group_3	0.118
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.063
r_symmetry_xyhbond_nbd_other	0.01
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5096
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	150

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Aimless	data scaling
PHASER	phasing