7VFQ | pdb_00007vfq

Wild type GltA from Bifidobacterium infantis JCM 1222 complexed with lacto-N-tetraose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z8F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293.15	30% (w/v) PEG MME 550, 10mM ZnSO4, 0.1M MES-NaOH (pH 5.5)

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.138	α = 97.41
b = 84.381	β = 92.25
c = 106.688	γ = 89.92

Symmetry
Space Group	P 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	PIXEL	DECTRIS EIGER X 16M		2016-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.55	47.59	95.5	0.075	0.106	0.075	0.97	5.8	1.8		187561			4.9

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	1.55	1.58	85.7		0.355	0.502	0.311	0.725	2	1.7

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	2Z8F	1.55	47.59	178122	9435	95.53	0.1927	0.1909	0.2	0.2271	0.23	RANDOM	10.99

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]
-0.07	0.06	-0.03	-0.63	-0.15	0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.504
r_dihedral_angle_3_deg	13.458
r_dihedral_angle_1_deg	6.302
r_dihedral_angle_4_deg	5.154
r_angle_refined_deg	1.694
r_angle_other_deg	1.54
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.504
r_dihedral_angle_3_deg	13.458
r_dihedral_angle_1_deg	6.302
r_dihedral_angle_4_deg	5.154
r_angle_refined_deg	1.694
r_angle_other_deg	1.54
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11940
Nucleic Acid Atoms
Solvent Atoms	1525
Heterogen Atoms	217

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

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.