6SYN | pdb_00006syn

Crystal structure of Y. pestis penicillin-binding protein 3

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		296	0.2 uL of protein (in 20 mM Tris-HCl pH 7.5 150 mM NaCl and 2 mM carbenicillin) at 6.7 mg/ml and 0.2 uL of precipitant (0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5 and 20% PEG 8000)

Crystal Properties
Matthews coefficient	Solvent content
2.04	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.86	α = 90
b = 104.95	β = 90
c = 110.42	γ = 90

Symmetry
Space Group	P 2 21 21

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	RIGAKU SATURN 944+		2017-01-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.63	36	98.7	0.122	0.153	0.097	0.971	7.8	3.9		14613			8.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.63	2.74	93.8		0.234	0.312	0.203	0.652	3.9	3.1

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	4BJP	2.63	36	13830	752	98.48	0.2118	0.2083	0.2136	0.273	0.2749	RANDOM	15.899

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			-0.46		0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.183
r_dihedral_angle_4_deg	19.034
r_dihedral_angle_3_deg	17.665
r_dihedral_angle_1_deg	6.951
r_angle_refined_deg	1.388
r_angle_other_deg	1.113
r_chiral_restr	0.06
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3596
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	8

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing