6VNU | pdb_00006vnu

X-ray Crystal Structure of Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme Complex with CTX-M-14 E166A Beta-Lactamase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XXR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.9	293.15	Potassium Phosphate

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.152	α = 90
b = 106.894	β = 101.68
c = 47.908	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 16M		2018-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

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	1.47	53.447	80.7	0.065	14.46	2.8		60469

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	1.47	1.51	93.7		0.452	2.06

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4XXR	1.47	34.16	49262	2519	69.03	0.1752	0.173	0.2181	RANDOM	14.953

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]
0.37		0.37	-0.51		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.697
r_dihedral_angle_3_deg	13.984
r_dihedral_angle_4_deg	12.494
r_dihedral_angle_1_deg	6.864
r_angle_refined_deg	1.737
r_angle_other_deg	1.511
r_chiral_restr	0.235
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.697
r_dihedral_angle_3_deg	13.984
r_dihedral_angle_4_deg	12.494
r_dihedral_angle_1_deg	6.864
r_angle_refined_deg	1.737
r_angle_other_deg	1.511
r_chiral_restr	0.235
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3896
Nucleic Acid Atoms
Solvent Atoms	525
Heterogen Atoms	97

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	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.