9S4Y | pdb_00009s4y

AcuB from Geobacillus stearothermophilus with Ap4A

X-RAY DIFFRACTION

---

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	10% PEG 20000, 100 mM MES pH 6.5, soaked over night in 10 mM Ap4A cryo: 10% PEG 20000, 15% PEG 400, 100 mM MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.61	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.295	α = 90
b = 96.954	β = 90
c = 101.709	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		2025-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	3.35	50	100	0.433	0.99	8	12.7		7877		-3	61.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.35	50	100		1.57	0.61	2	12.6

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	3.35	48.524	7865	402	99.975	0.231	0.2288	0.2328	0.2617	0.2687	83.038

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]
5.183			-3.01		-2.173

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.737
r_dihedral_angle_6_deg	11.017
r_lrange_it	5.387
r_lrange_other	5.387
r_dihedral_angle_1_deg	4.875
r_dihedral_angle_2_deg	4.231
r_scangle_it	3.076
r_scangle_other	3.075
r_mcangle_it	2.901
r_mcangle_other	2.9
r_scbond_it	1.696
r_scbond_other	1.696
r_mcbond_it	1.638
r_mcbond_other	1.638
r_angle_refined_deg	0.849
r_angle_other_deg	0.309
r_dihedral_angle_other_2_deg	0.284
r_nbd_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.172
r_nbd_other	0.171
r_symmetry_nbd_other	0.17
r_symmetry_nbd_refined	0.162
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.125
r_ncsr_local_group_1	0.1
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.041
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	3147
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	108

Software

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