4NU9 | pdb_00004nu9

2.30 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) from Staphylococcus aureus with BME-free Cys289

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MPB	PDB ENTRY 4MPB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	7 mg/mL protein in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 0.5 mM TCEP, crystallized using the JCSG+ Suite (D6: 0.2 M magnesium chloride, 0.1 M Tris, pH 8.5, 20% w/v PEG8000), VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.639	α = 90
b = 118.427	β = 90
c = 88.532	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD	beryllium lenses	2013-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	30	96.9	0.107	18.37	7.3	48647	48647		-3	30.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34	100		0.501	4.4	7.5	2474

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4MPB	2.3	29.87	46132	46132	2469	96.43	0.16215	0.15934	0.17	0.21538	0.22	RANDOM	25.281

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]
-0.08			-1.94		2.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.251
r_dihedral_angle_4_deg	15.877
r_dihedral_angle_3_deg	12.649
r_dihedral_angle_1_deg	3.921
r_angle_refined_deg	1.705
r_angle_other_deg	0.849
r_chiral_restr	0.103
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.251
r_dihedral_angle_4_deg	15.877
r_dihedral_angle_3_deg	12.649
r_dihedral_angle_1_deg	3.921
r_angle_refined_deg	1.705
r_angle_other_deg	0.849
r_chiral_restr	0.103
r_bond_refined_d	0.014
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	7729
Nucleic Acid Atoms
Solvent Atoms	605
Heterogen Atoms	4

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.