3BEC | pdb_00003bec

Crystal structure of E. coli penicillin-binding protein 5 in complex with a peptide-mimetic cephalosporin

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	294	100mM Tris pH 8.0, 8% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.5	α = 90
b = 50.5	β = 121.1
c = 85.4	γ = 90

Symmetry
Space Group	C 1 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	CCD	MARMOSAIC 300 mm CCD		2006-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97934	APS	22-ID

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	1.6	41	97.3	0.074	25.7	3.5	51428	51428

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	1.6	1.66	82.7		0.414	1.8	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 1NZO	1.6	40.82	51415	48813	2602	97.15	0.19328	0.19215	0.2	0.21473	0.22	RANDOM	16.458

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]
-0.7		-0.68	0.35		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.319
r_dihedral_angle_4_deg	13.97
r_dihedral_angle_3_deg	12.099
r_dihedral_angle_1_deg	5.675
r_sphericity_free	4.778
r_scangle_it	3.276
r_sphericity_bonded	2.323
r_scbond_it	2.32
r_mcangle_it	1.646
r_rigid_bond_restr	1.546
r_angle_refined_deg	1.295
r_mcbond_it	1.137
r_angle_other_deg	0.872
r_mcbond_other	0.405
r_nbd_refined	0.201
r_symmetry_vdw_other	0.194
r_nbd_other	0.191
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.148
r_symmetry_hbond_refined	0.137
r_symmetry_vdw_refined	0.13
r_nbtor_other	0.086
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2713
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
SERGUI	data collection
HKL-2000	data reduction
SCALEPACK	data scaling