9S50 | pdb_00009s50

AcuB from Geobacillus stearothermophilus with AMP 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
2.55	51.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.564	α = 90
b = 96.535	β = 90
c = 101.435	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	3.06	50	99.6	0.227	0.997	8.3	12.8		10462		-3	84

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	3.06	50	99.9		1.61	0.657	1.3	13.9

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	3.06	48.314	10027	513	99.741	0.226	0.2232	0.2251	0.2871	0.2896	126.787

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]
15.027			-6.894		-8.133

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.111
r_lrange_it	13.258
r_lrange_other	13.257
r_dihedral_angle_6_deg	11.603
r_mcangle_it	9.226
r_mcangle_other	9.224
r_scangle_it	8.796
r_scangle_other	8.795
r_dihedral_angle_1_deg	6.706
r_mcbond_it	5.791
r_mcbond_other	5.789
r_dihedral_angle_2_deg	5.498
r_scbond_it	5.268
r_scbond_other	5.267
r_angle_refined_deg	1.099
r_dihedral_angle_other_2_deg	0.451
r_angle_other_deg	0.365
r_symmetry_xyhbond_nbd_refined	0.251
r_nbd_other	0.225
r_symmetry_nbd_refined	0.22
r_nbd_refined	0.2
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.157
r_ncsr_local_group_1	0.095
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.049
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
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	6
Heterogen Atoms	121

Software

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