9S4W | pdb_00009s4w

AcuB from Geobacillus stearothermophilus without nucleotide

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	4041A1 10% PEG 20000, 100 mM MES pH 6.5, cryo: 10% PEG 20000, 15% PEG 400, 100 mM MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.21	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.618	α = 90
b = 96.777	β = 90
c = 98.97	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		2025-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	1.0596	PETRA III, EMBL c/o DESY	P13 (MX1)

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	50	100	0.109	0.113	0.031	0.999	20.7	13.1		30440		-3	35.7

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	2.05	100		1.176	1.224	0.338	0.82	2.8	12.8

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	48.435	30382	1465	99.977	0.193	0.1906	0.1923	0.2447	0.2468	38.967

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]
3.558			-1.932		-1.626

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.014
r_dihedral_angle_3_deg	14.951
r_dihedral_angle_6_deg	13.777
r_lrange_it	8.743
r_lrange_other	8.737
r_scangle_it	6.512
r_scangle_other	6.511
r_dihedral_angle_1_deg	6.407
r_mcangle_it	4.772
r_mcangle_other	4.772
r_scbond_it	4.232
r_scbond_other	4.23
r_mcbond_it	3.202
r_mcbond_other	3.201
r_angle_refined_deg	1.91
r_angle_other_deg	0.614
r_nbd_refined	0.238
r_symmetry_nbd_other	0.191
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.182
r_nbd_other	0.171
r_symmetry_xyhbond_nbd_refined	0.153
r_ncsr_local_group_1	0.142
r_symmetry_nbd_refined	0.131
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3190
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	16

Software

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