5EZ4 | pdb_00005ez4

2.11 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) P449M/Y450L double mutant from Staphylococcus aureus in complex with NAD+ and BME-modified 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	7	295	Potein: 6 mg/ml, 10 mM Tris-HCl, pH 8.3, 500 mM NaCl, 5 mM BME, 5mM NAD+. Crystallization: Classics II D3: 100 mM HEPES, pH 7.0, 30%(v/v) Jeffamine ED-2001. Cryo: crystallization condition

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 225.026	α = 90
b = 102.158	β = 104.85
c = 118.33	γ = 90

Symmetry
Space Group	C 1 2 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		2015-06-29	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	2.11	30	99.9	0.136	9.92	3.5		154078			21.3

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	2.11	2.15	99.5		0.496	2.06	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	2.11	29.69	141144	7478	99.87	0.14281	0.14113	0.15	0.17474	0.18	RANDOM	22.98

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]
0.94		-0.52	0.86		-1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.161
r_dihedral_angle_4_deg	16.825
r_dihedral_angle_3_deg	12.355
r_dihedral_angle_1_deg	4.637
r_angle_refined_deg	1.545
r_angle_other_deg	1.008
r_chiral_restr	0.098
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.006
r_bond_other_d	0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15364
Nucleic Acid Atoms
Solvent Atoms	2001
Heterogen Atoms	305

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
ARP	model building
PHASER	phasing
Coot	model building
BLU-MAX	data collection