3H76 | pdb_00003h76

Crystal structure of PqsD, a key enzyme in Pseudomonas aeruginosa quinolone signal biosynthesis pathway

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HN9	PDB entry 1HN9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.16 M MgCl2, 0.08M Tris-HCl pH 8.5, 24% PEG 4000, 20% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.081	α = 90
b = 90.42	β = 95.38
c = 67.894	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	IMAGE PLATE	MAR scanner 345 mm plate		2008-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	27	91.4	0.091	5.1	3.1		49952

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	88.3		0.51	1.6	3.07

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 1HN9	1.8	25.6	47404	2528	91.38	0.20167	0.19822	0.21	0.26593	0.27	RANDOM	34.725

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]
0.51		-0.18	-0.12		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.467
r_dihedral_angle_4_deg	19.042
r_dihedral_angle_3_deg	16.97
r_sphericity_free	9.156
r_dihedral_angle_1_deg	7.401
r_sphericity_bonded	4.382
r_scangle_it	4.236
r_scbond_it	3.03
r_rigid_bond_restr	2.031
r_mcangle_it	1.926
r_angle_refined_deg	1.913
r_mcbond_it	1.312
r_symmetry_vdw_refined	0.313
r_nbtor_refined	0.306
r_xyhbond_nbd_refined	0.259
r_nbd_refined	0.241
r_symmetry_hbond_refined	0.238
r_chiral_restr	0.128
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5007
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling