3H77

Crystal structure of Pseudomonas aeruginosa PqsD in a covalent complex with anthranilate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H76	PDB entry 3H76

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.2 M MgCl2, 0.1M Tris-HCl pH 8.5, 21% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.894	α = 90
b = 59.656	β = 103.95
c = 83.427	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	100	CCD	ADSC QUANTUM 315		2009-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0809	NSLS	X29A

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	1.8	50	99.7	0.068	7.8	7		59980

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)
	1.8	1.86	99.3		0.402	6.2	6.1

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 3H76	1.8	30	56914	3026	99.63	0.15409	0.15186	0.19488	RANDOM	25.632

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]
-0.06		0.06	0.16		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.851
r_dihedral_angle_4_deg	17.561
r_dihedral_angle_3_deg	13.973
r_dihedral_angle_1_deg	6.796
r_sphericity_free	4.501
r_scangle_it	3.401
r_scbond_it	3.074
r_rigid_bond_restr	2.897
r_sphericity_bonded	2.82
r_angle_refined_deg	1.663
r_mcangle_it	1.46
r_mcbond_it	1.15
r_nbtor_refined	0.305
r_nbd_refined	0.228
r_symmetry_vdw_refined	0.213
r_symmetry_hbond_refined	0.181
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.142
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5160
Nucleic Acid Atoms
Solvent Atoms	582
Heterogen Atoms	114

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling