6XV5 | pdb_00006xv5

Crystal structure of penicillin-binding protein 2 from Yersinia pestis in complex with ertapenem

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TII

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		296	Crystals were grown in a condition containing 1 uL of 1 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM ertapenem) and 2 uL of reservoir solution (0.5 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5).

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.265	α = 90
b = 147.772	β = 90
c = 164.523	γ = 90

Symmetry
Space Group	P 21 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	PIXEL	DECTRIS EIGER X 16M		2018-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.67	109.937	100	0.133	0.999	12.2	13.1		38541

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.701	7.331			0.04	0.999

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6TII	2.673	109.937	30718	1485	77.249	0.216	0.213	0.22	0.2851	0.28	77.799

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]
0.278			0.125		-0.402

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.947
r_dihedral_angle_4_deg	17.948
r_dihedral_angle_3_deg	17.737
r_dihedral_angle_1_deg	9.792
r_lrange_it	8.551
r_lrange_other	8.51
r_mcangle_it	5.381
r_mcangle_other	5.38
r_scangle_it	4.707
r_scangle_other	4.707
r_mcbond_it	3.194
r_mcbond_other	3.191
r_scbond_other	2.659
r_scbond_it	2.658
r_angle_refined_deg	1.279
r_angle_other_deg	1.102
r_nbd_other	0.244
r_nbd_refined	0.195
r_symmetry_nbd_other	0.193
r_symmetry_nbd_refined	0.187
r_nbtor_refined	0.158
r_xyhbond_nbd_refined	0.157
r_chiral_restr_other	0.118
r_ncsr_local_group_1	0.112
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_other	0.077
r_symmetry_xyhbond_nbd_refined	0.069
r_chiral_restr	0.053
r_gen_planes_refined	0.005
r_bond_refined_d	0.003
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8499
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
PHASES	phasing