3M2K

Crystal Structure of fluorescein-labeled Class A -beta lactamase PenP in complex with cefotaxime

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BLM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	291	PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.538	α = 90
b = 91.524	β = 104.22
c = 66.302	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray					2007-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

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	46		0.148				18395

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	4BLM	3.5	40.23	5798	308	94.92	0.17952	0.1763	0.2359	RANDOM	13.684

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]
-1.97		-1.38	4.27		-2.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.384
r_dihedral_angle_3_deg	24.733
r_dihedral_angle_4_deg	23.554
r_dihedral_angle_1_deg	11.388
r_scangle_it	4.06
r_angle_refined_deg	3.999
r_scbond_it	2.666
r_mcangle_it	1.426
r_mcbond_it	1.061
r_nbtor_refined	0.355
r_nbd_refined	0.346
r_symmetry_vdw_refined	0.25
r_chiral_restr	0.243
r_symmetry_hbond_refined	0.239
r_xyhbond_nbd_refined	0.236
r_bond_refined_d	0.051
r_gen_planes_refined	0.021
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3873
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	52

Software

Software
Software Name	Purpose
CrystalClear	data collection
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling