3CNM | pdb_00003cnm

Crystal Structure of Phenazine Biosynthesis Protein PhzA/B from Burkholderia cepacia R18194, DHHA complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B4O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	285	16-20% (w/v) PEG3350, 0.2 M NH4OAc, 0.1 M Bis-Tris pH 6.1-6.7; complex prepared by overnight soaking in mother liquor containing 50 mM DHHA, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.09	α = 90
b = 65.09	β = 90
c = 161.55	γ = 120

Symmetry
Space Group	P 32 2 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	MARMOSAIC 225 mm CCD	SI(111) monochromator	2008-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9809	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.65	20	100	0.066	0.139	16	14.1	48683	48675		3	33

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	1.65	1.75	100		0.42	3.7	13.3	7754

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	rigid body refinement of apo structure	THROUGHOUT	3B4O	1.65	19.81	46189	2447	99.99	0.15662	0.15469	0.17	0.1939	0.2	RANDOM	24.467

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	36.323
r_dihedral_angle_4_deg	19.758
r_dihedral_angle_3_deg	14.549
r_dihedral_angle_1_deg	6.014
r_scangle_it	5.686
r_scbond_it	4
r_mcangle_it	2.457
r_angle_refined_deg	2.319
r_mcbond_it	2.205
r_angle_other_deg	1.103
r_mcbond_other	0.53
r_symmetry_vdw_refined	0.41
r_symmetry_hbond_refined	0.361
r_symmetry_vdw_other	0.342
r_nbd_refined	0.241
r_nbd_other	0.223
r_xyhbond_nbd_refined	0.222
r_nbtor_refined	0.19
r_chiral_restr	0.162
r_nbtor_other	0.089
r_bond_refined_d	0.031
r_gen_planes_refined	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2619
Nucleic Acid Atoms
Solvent Atoms	377
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
XDS	data reduction
XSCALE	data scaling