2JCH

Structural and mechanistic basis of penicillin binding protein inhibition by lactivicins

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BG1	PDB ENTRY 2BG1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		50 MM HEPES PH 7 3.2 M NACL 0.8 M AMMONIUM SULFATE

Crystal Properties
Matthews coefficient	Solvent content
3.5	67.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.84	α = 90
b = 143.58	β = 90
c = 97.44	γ = 90

Symmetry
Space Group	C 2 2 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	MARRESEARCH		2006-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	2.4	19.9	99.3	0.09	12.9	5.2		29294		3

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	2.4	2.6	100		0.43	2.9	4.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2BG1	2.4	85.13	27860	1434	99.3	0.206	0.203	0.262	RANDOM	29.7

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]
1.79			-0.04		-1.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.168
r_dihedral_angle_3_deg	20.094
r_dihedral_angle_4_deg	19.537
r_dihedral_angle_1_deg	8.299
r_scangle_it	4.863
r_scbond_it	3.347
r_angle_refined_deg	2.398
r_mcangle_it	2.18
r_mcbond_it	1.321
r_symmetry_vdw_refined	0.474
r_symmetry_hbond_refined	0.341
r_nbtor_refined	0.312
r_nbd_refined	0.247
r_xyhbond_nbd_refined	0.2
r_chiral_restr	0.156
r_bond_refined_d	0.028
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3550
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
AMoRE	phasing