9S4X | pdb_00009s4x

AcuB from Geobacillus stearothermophilus with 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	10% PEG 20000, 100 mM MES pH 6.5, soaked in 10 mM ADP cryo: 10% PEG 20000, 15% PEG 400, 100 mM MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.59	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.486	α = 90
b = 96.492	β = 90
c = 101.088	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 PILATUS3 6M		2025-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	1.05960	PETRA III, EMBL c/o DESY	P13 (MX1)

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	2.76	50	99.5	0.128	0.998	12.8	6.9		26470		-3	63.7

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	2.76	3.02	99.3		0.527	0.906	2.8	6.8

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	2.76	48.293	13752	631	99.964	0.186	0.1828	0.1808	0.2489	0.2469	70.457

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]
6.752			-2.871		-3.882

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.369
r_dihedral_angle_6_deg	13.243
r_lrange_it	10.366
r_lrange_other	10.355
r_dihedral_angle_2_deg	8.504
r_scangle_it	8.289
r_scangle_other	8.288
r_mcangle_it	7.031
r_mcangle_other	7.03
r_dihedral_angle_1_deg	6.98
r_scbond_it	5.719
r_scbond_other	5.717
r_mcbond_it	4.795
r_mcbond_other	4.782
r_angle_refined_deg	1.755
r_angle_other_deg	0.553
r_symmetry_nbd_refined	0.315
r_nbd_other	0.27
r_nbd_refined	0.245
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.152
r_ncsr_local_group_1	0.108
r_symmetry_xyhbond_nbd_refined	0.105
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_dihedral_angle_other_2_deg	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	3137
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	124

Software

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