7L5V | pdb_00007l5v

Crystal Structure of the Class D Beta-lactamase OXA-935 from Pseudomonas aeruginosa, Monoclinic Crystal Form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E3U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	292	Protein: 6.0 mg/ml, 0.01M Tris pH 8.3; Screen - Classics II (G9): 0.2M Ammonium acetate, 0.1M Tris pH 8.5, 25% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.074	α = 90
b = 75.043	β = 91.93
c = 82.746	γ = 90

Symmetry
Space Group	P 1 21 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 9M	Be	2020-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.12713	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.3	30	91.2	0.072	0.079	0.033	0.997	20.6	5.6		126515		-3	10.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32	74		0.517	0.517	0.575	0.247	0.854	3.3	4.9

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	1E3U	1.3	23.95	119981	6069	91.31	0.1502	0.1492	0.15	0.1699	0.17	RANDOM	15.778

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]
0.42		-1.17	0.09		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.736
r_dihedral_angle_4_deg	12.682
r_dihedral_angle_3_deg	9.189
r_dihedral_angle_1_deg	3.825
r_angle_refined_deg	1.287
r_rigid_bond_restr	0.694
r_angle_other_deg	0.327
r_chiral_restr	0.062
r_gen_planes_refined	0.056
r_gen_planes_other	0.049

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.736
r_dihedral_angle_4_deg	12.682
r_dihedral_angle_3_deg	9.189
r_dihedral_angle_1_deg	3.825
r_angle_refined_deg	1.287
r_rigid_bond_restr	0.694
r_angle_other_deg	0.327
r_chiral_restr	0.062
r_gen_planes_refined	0.056
r_gen_planes_other	0.049
r_bond_refined_d	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3881
Nucleic Acid Atoms
Solvent Atoms	725
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	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.