4I61

Crystal structure of a trimeric bacterial microcompartment shell protein PduB

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	292	0.1 M sodium cacodylate, 1.4 M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.01	α = 90
b = 119.55	β = 90
c = 147.09	γ = 90

Symmetry
Space Group	C 2 2 21

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 315r		2012-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	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	1.64	59.77	99.8	0.131	0.074	0.102	4.9		74480		9.6	9.916

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	1.64	1.68	99.8		0.703	0.393	2.2	4.9	26795

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4FAY	1.64	59.77	98878	70684	3749	99.77	0.15519	0.15519	0.15279	0.20028	RANDOM	11.795

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]
-0.02					0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.288
r_dihedral_angle_4_deg	14.812
r_dihedral_angle_3_deg	12.549
r_dihedral_angle_1_deg	6.622
r_scangle_it	5.595
r_scbond_it	3.418
r_angle_refined_deg	1.982
r_mcangle_it	1.92
r_mcbond_it	1.244
r_chiral_restr	0.15
r_bond_refined_d	0.025
r_gen_planes_refined	0.011
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	4989
Nucleic Acid Atoms
Solvent Atoms	780
Heterogen Atoms

Software

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