3ITB | pdb_00003itb

Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in complex with a substrate fragment

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IT9	apo PBP6 model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	292	PEG 8000, pH 4.5, vapor diffusion, hanging drop, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.534	α = 90
b = 185.351	β = 100.99
c = 82.329	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	CCD	ADSC QUANTUM Q315r	mirrors	2009-04-10		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11587	ALS	8.3.1

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	1.8	50	88	0.07	16.5	2.2		136723

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	1.8	1.86	84		0.59		2.2	12997

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	apo PBP6 model	1.8	40.2	136655	6831	87.84	0.207	0.205	0.2	0.254	0.25	RANDOM	38.923

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]
2.8		0.27	-2.87		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.959
r_dihedral_angle_3_deg	19.198
r_dihedral_angle_4_deg	18.584
r_dihedral_angle_1_deg	14.318
r_scangle_it	8.051
r_scbond_it	5.261
r_mcangle_it	3.512
r_mcbond_it	2.29
r_angle_refined_deg	1.733
r_chiral_restr	0.178

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.959
r_dihedral_angle_3_deg	19.198
r_dihedral_angle_4_deg	18.584
r_dihedral_angle_1_deg	14.318
r_scangle_it	8.051
r_scbond_it	5.261
r_mcangle_it	3.512
r_mcbond_it	2.29
r_angle_refined_deg	1.733
r_chiral_restr	0.178
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10613
Nucleic Acid Atoms
Solvent Atoms	699
Heterogen Atoms	53

Software

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