9S52 | pdb_00009s52

AcuB from Geobacillus stearothermophilus with AMP

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 10 mM AMP 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 = 52.686	α = 90
b = 96.414	β = 90
c = 101.867	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	2024-03-15	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	2.3	50	100	0.276	0.996	11.7	12.9		23740		-3	41.4

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	2.3	2.49	100		1.549	0.537	2	13.6

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	2.3	48.254	23730	1248	99.971	0.202	0.1997	0.2023	0.25	0.2509	45.518

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]
1.02			0.588		-1.608

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.552
r_dihedral_angle_6_deg	14.292
r_lrange_it	10.72
r_lrange_other	10.68
r_dihedral_angle_2_deg	9.737
r_dihedral_angle_1_deg	7.089
r_scangle_it	6.086
r_scangle_other	6.085
r_mcangle_it	5.479
r_mcangle_other	5.478
r_scbond_it	3.794
r_scbond_other	3.793
r_mcbond_it	3.495
r_mcbond_other	3.494
r_angle_refined_deg	1.747
r_angle_other_deg	0.553
r_symmetry_xyhbond_nbd_other	0.261
r_symmetry_nbd_refined	0.236
r_nbd_refined	0.221
r_nbd_other	0.217
r_xyhbond_nbd_refined	0.199
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.121
r_ncsr_local_group_1	0.101
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.076
r_dihedral_angle_other_2_deg	0.015
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	3180
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	108

Software

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