2PFZ | pdb_00002pfz

Crystal structure of DctP6, a Bordetella pertussis extracytoplasmic solute receptor binding pyroglutamic acid

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	36% (w/v) PEG 2000 MME, 0.1M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.39	α = 90
b = 108.39	β = 90
c = 63.09	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	MAR CCD 165 mm		2006-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.97942	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	19.85				35380	35219

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.8	19.85	35219	1765	99.66	0.189	0.187	0.19	0.236	0.24	RANDOM	22.257

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.563
r_dihedral_angle_4_deg	20.974
r_dihedral_angle_3_deg	15.882
r_dihedral_angle_1_deg	5.919
r_sphericity_free	5.235
r_scangle_it	3.517
r_scbond_it	2.618
r_sphericity_bonded	2.481
r_rigid_bond_restr	1.999
r_mcangle_it	1.476
r_angle_refined_deg	1.435
r_mcbond_it	0.99
r_nbtor_refined	0.302
r_nbd_refined	0.218
r_symmetry_vdw_refined	0.168
r_symmetry_hbond_refined	0.138
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.116
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2349
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction
XSCALE	data scaling
AMoRE	phasing