5OJ0 | pdb_00005oj0

Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae in complex with Cefepime

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K25

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	290	2.3-3.0 M NaCl, 0.1 M sodium acetate pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.547	α = 90
b = 99.547	β = 90
c = 189.66	γ = 120

Symmetry
Space Group	P 31 2 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 6M		2015-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97947	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.66	39.24	99.6	0.16	0.12	5.7	4.2		31872

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.66	2.76	99.6		0.8	0.69		4.3

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	1k25	2.66	39.24	30354	1621	99.93	0.17477	0.17165	0.18	0.23143	0.23	RANDOM	64.555

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]
-0.14	-0.07		-0.14		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.387
r_dihedral_angle_3_deg	19.85
r_dihedral_angle_4_deg	15.192
r_long_range_B_other	13.936
r_long_range_B_refined	13.935
r_scangle_other	10.205
r_mcangle_it	9.637
r_mcangle_other	9.636
r_dihedral_angle_1_deg	8.409
r_scbond_it	7.003
r_scbond_other	7.002
r_mcbond_it	6.611
r_mcbond_other	6.606
r_angle_refined_deg	2.013
r_angle_other_deg	1.189
r_chiral_restr	0.125
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	5057
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
Coot	model building