7AJX | pdb_00007ajx

The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with meropenem

X-RAY DIFFRACTION

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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	0.1M HEPES pH 7 + 10% PEG 8000 + 10% Ethylene Glycol

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.877	α = 90
b = 101.224	β = 90
c = 115.285	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		2017-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979160	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	2.55	46.386	99.9	0.068	0.997	9.2	6.7		22790

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	2.55	2.66	99.9		1.038	0.516	1	6.8

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7AJ9	2.55	46.34	22737	1104	99.838	0.212	0.209	0.22	0.267	0.27	64.039

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]
-5.689			0.087		5.602

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.661
r_dihedral_angle_4_deg	20.052
r_dihedral_angle_3_deg	16.968
r_lrange_it	9.491
r_lrange_other	9.49
r_scangle_it	7.476
r_scangle_other	7.475
r_dihedral_angle_1_deg	7.293
r_mcangle_it	6.335
r_mcangle_other	6.335
r_scbond_it	4.704
r_scbond_other	4.703
r_mcbond_it	4.14
r_mcbond_other	4.139
r_angle_refined_deg	1.452
r_angle_other_deg	1.188
r_symmetry_xyhbond_nbd_refined	0.227
r_nbd_other	0.226
r_nbd_refined	0.216
r_symmetry_nbd_other	0.193
r_symmetry_nbd_refined	0.191
r_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.166
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.068
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_symmetry_xyhbond_nbd_other	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3992
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing