7UHM | pdb_00007uhm

Time-Resolved Structure of Metallo Beta-Lactamase L1 in a Complex with Cleaved Moxalactam (150 ms Snapshot)

X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7L91

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		289	Batch crystallization done in polypropylene tubes. 200 ul of the L1 (48 mg/ml) in a buffer 0.015 Tris, 0.1 M KCl, 1.5 mM TCEP, 5 mM ZnCl2 pH 7.0 was added to 200 ul of 0.15 M sodium malonate pH 8.0, 20% (w/v) PEG3350.

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.853	α = 90
b = 105.853	β = 90
c = 99.1	γ = 120

Symmetry
Space Group	P 64 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	295	CCD	RAYONIX MX340-HS		2020-03-03	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	1.02-1.15	APS	14-ID-B

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	Nylon Mesh	fixed target

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Details	Sample Solvent
1	ALEX mesh holder	nylon mesh	xyz stage	SmarAct Motors viaPMAC start/stop raster over area

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1	316	2847	316

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	2.2	34.65	71	0.136	23	15.3		12098			12.79

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	2.2	2.3			0.103

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7L91	2.7	34.65	8383	396	88.61	0.2376	0.235	0.23	0.2901	0.29	22.27

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.9262
f_angle_d	0.5431
f_chiral_restr	0.041
f_plane_restr	0.0044
f_bond_d	0.0025

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1986
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	26

Software

Software
Software Name	Purpose
PHENIX	refinement
MOLREP	phasing
Precognition	data reduction
Epinorm	data scaling

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.