4QN2 | pdb_00004qn2

2.6 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) G234S mutant from Staphylococcus aureus (IDP00699) in complex with NAD+ and 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, 2 mM NAD+, crystallization: The Classics II Suite (G9): 0.2 M ammonium acetate, 0.1 M Tris, pH 8.5, 25% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.592	α = 90
b = 168.368	β = 104.92
c = 144.523	γ = 90

Symmetry
Space Group	P 1 21 1

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	2013-10-14	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	2.6	30	93.7	0.104	12.8	3.9	117959	117959		-3	51.9

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	2.6	2.64	97.1		0.607	2.34	3.8	6068

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	2.6	29.78	111581	111581	5916	93.61	0.18605	0.18427	0.18	0.21925	0.22	RANDOM	42.282

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]
-3.83		-1.07	-2.48		5.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.843
r_dihedral_angle_3_deg	11.426
r_dihedral_angle_4_deg	10.629
r_dihedral_angle_1_deg	2.531
r_angle_refined_deg	1.587
r_angle_other_deg	1.136
r_chiral_restr	0.097
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.843
r_dihedral_angle_3_deg	11.426
r_dihedral_angle_4_deg	10.629
r_dihedral_angle_1_deg	2.531
r_angle_refined_deg	1.587
r_angle_other_deg	1.136
r_chiral_restr	0.097
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	30828
Nucleic Acid Atoms
Solvent Atoms	702
Heterogen Atoms	356

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.