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Crystal Structure of Moonlighting GAPDH protein of Lactobacillus gasseri

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LVF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	0.1 M sodium cacodylate pH 6.5, 16% (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.922	α = 90
b = 114.922	β = 90
c = 118.62	γ = 90

Symmetry
Space Group	I 41 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	VERTICALLY COLLIMATING PREMIRROR, TOROIDAL FOCUSING MIRROR	2016-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13C1	0.97622	NSRRC	BL13C1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.88	30	98.8	0.067	0.07	0.02	41.7	12		32168			32

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.88	1.95	94.8		0.546	0.572	0.165	0.96	3.7	10.5

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 (All)	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	3LVF	1.88	29.673	32038	1625	98.469	0.138	0.1344	0.13	0.217	0.22	RANDOM	44.881

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]
-0.676			-0.676		1.352

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.332
r_dihedral_angle_3_deg	15.383
r_dihedral_angle_4_deg	15.22
r_lrange_it	7.845
r_dihedral_angle_1_deg	7.762
r_scangle_it	7.539
r_scbond_it	7.192
r_rigid_bond_restr	6.538
r_mcangle_it	6.164
r_mcbond_it	5.384
r_angle_refined_deg	1.404
r_nbtor_refined	0.316
r_nbd_refined	0.219
r_symmetry_xyhbond_nbd_refined	0.191
r_xyhbond_nbd_refined	0.161
r_symmetry_nbd_refined	0.154
r_chiral_restr	0.099
r_gen_planes_refined	0.011
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2534
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	48

Software

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