3PAC | pdb_00003pac

Crystal structure of PduT a trimeric bacterial microcompartment protein with 4Fe-4S cluster binding site

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	292	0.1M NaCl, 0.1M Bicine, 25% PEG 550, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.68	α = 90
b = 67.68	β = 90
c = 62.03	γ = 120

Symmetry
Space Group	P 63

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 210		2009-10-30	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2010-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.933	ESRF	ID14-1
2	SYNCHROTRON	DIAMOND BEAMLINE I04	1.1410	Diamond	I04

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
1,2	1.86	33.84	100	0.035	0.095	18.5	8.2	13647	13647			21.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.86	1.96	98		0.22	0.58	3.7	8	1979

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.86	29.71	13647	12258	1372	99.96	0.20394	0.19862	0.2	0.2515	0.25	RANDOM	25.825

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	42.079
r_dihedral_angle_3_deg	19.148
r_dihedral_angle_4_deg	14.685
r_dihedral_angle_1_deg	6.358
r_scangle_it	6.323
r_scbond_it	4.03
r_mcangle_it	2.391
r_angle_refined_deg	2.068
r_mcbond_it	1.381
r_chiral_restr	0.137
r_bond_refined_d	0.023
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	1317
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
PHENIX	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing