5E31 | pdb_00005e31

2.3 Angstrom Crystal Structure of the Monomeric Form of Penicillin Binding Protein 2 Prime from Enterococcus faecium.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DVY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	Protein: 13.9 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3), 5mM Penicillin V; Screen: Classics II (H7), 0.15M DL-Malic acid (pH 7.0), 20% (w/v) PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.44	α = 90
b = 64.34	β = 90
c = 182.786	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	CCD	MARMOSAIC 225 mm CCD		2015-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.3	29.12	99.8	0.131	0.131	22.4	7		33135		-3	38.2

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	2.3	2.34	100		0.637	3.3	7.2

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	5DVY	2.3	29.12	30970	1677	98.77	0.19925	0.19676	0.21	0.24445	0.25	RANDOM	45.23

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]
-1.47			-3.71		5.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.115
r_dihedral_angle_3_deg	10.362
r_dihedral_angle_4_deg	8.619
r_long_range_B_refined	7.351
r_long_range_B_other	7.34
r_scangle_other	4.822
r_mcangle_it	4.153
r_mcangle_other	4.153
r_scbond_it	3.013
r_scbond_other	3.012
r_dihedral_angle_1_deg	2.825
r_mcbond_other	2.617
r_mcbond_it	2.616
r_angle_refined_deg	1.517
r_angle_other_deg	0.751
r_chiral_restr	0.09
r_gen_planes_refined	0.022
r_gen_planes_other	0.019
r_bond_refined_d	0.011
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4898
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
BLU-MAX	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing