3P2Y

Crystal structure of alanine dehydrogenase/pyridine nucleotide transhydrogenase from Mycobacterium smegmatis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L7D	PDB entry 1L7D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	21.6 mg/mL MysmA.00681.a.A1 PS00596 against PACT screen condition C11 20% PEG 6000, 0.1 M Hepes pH 7.0, 0.2 M CaCl2, cryo-protected with 25% ethylene glycol, crystal tracking ID 215904c11, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.76	α = 90
b = 89.76	β = 90
c = 179.57	γ = 120

Symmetry
Space Group	P 61 2 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	ADSC QUANTUM 315r		2010-08-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97946	ALS	5.0.1

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	1.82	50	97.8	0.052	42.32	17.3		38305		-3	23.517

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	1.82	1.87	81.2		0.234	11.1	14.1	2842

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1L7D	1.82	40.15	38192	1913	97.56	0.1665	0.165	0.1963	RANDOM	19.0145

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]
-0.37	-0.18		-0.37		0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.044
r_dihedral_angle_4_deg	22.038
r_dihedral_angle_3_deg	11.042
r_dihedral_angle_1_deg	5.184
r_scangle_it	4.225
r_scbond_it	2.414
r_mcangle_it	1.509
r_angle_refined_deg	1.428
r_mcbond_it	0.845
r_chiral_restr	0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.044
r_dihedral_angle_4_deg	22.038
r_dihedral_angle_3_deg	11.042
r_dihedral_angle_1_deg	5.184
r_scangle_it	4.225
r_scbond_it	2.414
r_mcangle_it	1.509
r_angle_refined_deg	1.428
r_mcbond_it	0.845
r_chiral_restr	0.102
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2462
Nucleic Acid Atoms
Solvent Atoms	376
Heterogen Atoms	12

Software

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

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.