3MZF | pdb_00003mzf

Structure of penicillin-binding protein 5 from E. coli: imipenem acyl-enzyme complex

X-RAY DIFFRACTION

---

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	7	294	100 MM TRIS PH 7.0, 8 % PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.78	α = 90
b = 50.35	β = 120.16
c = 84.29	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		2004-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-ID

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	1.5	33	96.6	0.055	0.055	40.1	6.8	61886	61886			20.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.55	76.3		0.488	0.488	1.8	3.9	4880

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 (All)	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	1.5	32.97	61823	61823	3123	96.7	0.189	0.189	0.188	0.19	0.212	0.21	RANDOM	22.92

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]
-0.16		-0.41	-0.56		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.07
r_dihedral_angle_4_deg	18.226
r_dihedral_angle_3_deg	11.55
r_dihedral_angle_1_deg	5.506
r_rigid_bond_restr	5.095
r_scbond_it	4.443
r_scangle_it	3.948
r_sphericity_free	3.375
r_sphericity_bonded	3.37
r_mcangle_it	1.496
r_angle_refined_deg	1.225
r_mcbond_it	1.021
r_nbtor_refined	0.301
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.115
r_xyhbond_nbd_refined	0.105
r_symmetry_hbond_refined	0.09
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2740
Nucleic Acid Atoms
Solvent Atoms	369
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
MAR345	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing