3D0K

Crystal structure of the LpqC, poly(3-hydroxybutyrate) depolymerase from Bordetella parapertussis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	1.6 M Ammonium sulfate, 0.1 M MES pH 6.5, 10% Dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.879	α = 90
b = 83.71	β = 92.68
c = 90.792	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	Mirrors	2008-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97920	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.83	41.83	99.8	0.12	8.5	4.5	54978	54978			20.67

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.83	1.86	99.7		0.598	2	3.8	2697

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.83	41.83	52230	52230	2803	99.69	0.166	0.166	0.164	0.209	RANDOM	24.02

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]
-0.88		-0.37	1.35		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.634
r_dihedral_angle_4_deg	19.518
r_dihedral_angle_3_deg	15.257
r_dihedral_angle_1_deg	6.211
r_scangle_it	4.704
r_scbond_it	3.075
r_mcangle_it	1.705
r_angle_refined_deg	1.639
r_mcbond_it	1.077
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.237
r_nbd_refined	0.207
r_symmetry_hbond_refined	0.182
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.119
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
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	4530
Nucleic Acid Atoms
Solvent Atoms	439
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXD	phasing
RESOLVE	phasing
Coot	model building