4KQO

Crystal structure of penicillin-binding protein 3 from pseudomonas aeruginosa in complex with piperacillin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OCL	PDB ENTRY 3OCL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	2.5 M NaCl; 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.049	α = 71.26
b = 74.935	β = 86.04
c = 82.785	γ = 85.59

Symmetry
Space Group	P 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 PILATUS 2M		2011-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91730	Diamond	I04-1

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	2.31	50	97.8	0.185	6	9.4		55461		-1.5

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	2.31	2.39	87.2		0.275	1.5	5.9	4929

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	PDB ENTRY 3OCL	2.31	47.1	52657	2804	97.81	0.2188	0.21714	0.24965	RANDOM	42.412

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]
1.07	0.93	0.85	1.26	2.32	-1.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.167
r_dihedral_angle_3_deg	14.911
r_dihedral_angle_4_deg	14.505
r_dihedral_angle_1_deg	5.685
r_angle_refined_deg	1.271
r_angle_other_deg	0.861
r_chiral_restr	0.066
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.167
r_dihedral_angle_3_deg	14.911
r_dihedral_angle_4_deg	14.505
r_dihedral_angle_1_deg	5.685
r_angle_refined_deg	1.271
r_angle_other_deg	0.861
r_chiral_restr	0.066
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7635
Nucleic Acid Atoms
Solvent Atoms	276
Heterogen Atoms	97

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	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.