7AJZ

The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with NAG-NAM(tetrapeptide)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7AJ9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298	0.1 M HEPES pH 7 + 10% PEG 8000 + 10% Ethylene Glycol

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.51	α = 90
b = 92.558	β = 90
c = 276.064	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS 6M		2017-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979080	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.98	48.9	100	0.047	0.998	10	10.9		31171

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.98	3.14	100		1.265	0.405	11.5	11.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7AJ9	2.98	48.9	29567	1537	99.96	0.2123	0.2095	0.2663	RANDOM	114.317

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]
0.36			-1.18		0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.927
r_dihedral_angle_3_deg	16.193
r_dihedral_angle_4_deg	14.702
r_dihedral_angle_1_deg	6.815
r_angle_refined_deg	1.367
r_angle_other_deg	1.181
r_chiral_restr	0.056
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.927
r_dihedral_angle_3_deg	16.193
r_dihedral_angle_4_deg	14.702
r_dihedral_angle_1_deg	6.815
r_angle_refined_deg	1.367
r_angle_other_deg	1.181
r_chiral_restr	0.056
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7890
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	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.