9S51 | pdb_00009s51

AcuB from Geobacillus stearothermophilus with ADP and ATP

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 30 min in 5 mM AMP + 5 mM ATP cryo: 10% PEG 20000, 15% PEG 400, 100 mM MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.59	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.433	α = 90
b = 96.513	β = 90
c = 101.157	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	double mirror	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	2.53	50	100	0.17	0.999	12.4	13.6		17740		-3	67.4

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	2.53	2.76	100		1.085	0.836	2.4	13.1

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	2.53	48.303	17738	873	99.921	0.195	0.1922	0.1931	0.2434	0.2454	81.911

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]
5.079			-1.788		-3.291

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.225
r_dihedral_angle_6_deg	14.631
r_lrange_it	12.431
r_lrange_other	12.43
r_scangle_it	10.191
r_scangle_other	10.189
r_mcangle_it	9.14
r_mcangle_other	9.139
r_dihedral_angle_2_deg	8.121
r_scbond_it	7.212
r_scbond_other	7.211
r_dihedral_angle_1_deg	7.2
r_mcbond_it	6.476
r_mcbond_other	6.476
r_angle_refined_deg	1.864
r_angle_other_deg	0.569
r_symmetry_nbd_refined	0.345
r_nbd_other	0.287
r_nbd_refined	0.231
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.149
r_ncsr_local_group_1	0.1
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.079
r_dihedral_angle_other_2_deg	0.076
r_symmetry_xyhbond_nbd_refined	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3127
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	125

Software

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