4KQQ | pdb_00004kqq

CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH (5S)-Penicilloic Acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OCL	PDB ENTRY 3OCL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	2.5 M NaCl; 0.1 M imidazole , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.931	α = 71.6
b = 74.168	β = 86.05
c = 82.121	γ = 85.85

Symmetry
Space Group	P 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		2011-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.97880	Diamond	I24

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	2.1	50	90.6	0.085	7.7	1.5		66325		-1.5

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	2.11	2.19	83.4		0.345	1.5	1.4	6071

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	PDB ENTRY 3OCL	2.1	46.98	62968	3357	90.02	0.20568	0.20353	0.2	0.24612	0.25	RANDOM	35.16

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]
-0.34	0.29	0.76	1.68	2.49	-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.411
r_dihedral_angle_4_deg	16.243
r_dihedral_angle_3_deg	12.887
r_dihedral_angle_1_deg	5.475
r_angle_refined_deg	1.147
r_chiral_restr	0.077
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
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	7767
Nucleic Acid Atoms
Solvent Atoms	424
Heterogen Atoms	112

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling