3M4B

A Zn-mediated tetrahedral protein lattice cage

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	25% PEG 1500, 0.1 M Bis-Tris, 0.2 M CaCl2 and 5 mM ZnCl2., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.363	α = 90
b = 125.363	β = 90
c = 164.509	γ = 120

Symmetry
Space Group	H 3 2

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 325 mm CCD	Flat collimating mirror, double crystal monochromator, toroid focusing mirror	2009-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.18	SSRL	BL9-2

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	2.5	90.614	100	0.106	0.106	16.5	6	17431	17431

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)
	2.5	2.64	100		0.481	0.481	1.5	5.4	2495

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.5	41.27	16174	1257	99.98	0.20206	0.19791	0.25558	RANDOM	34.565

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]
-0.21	-0.1		-0.21		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.975
r_dihedral_angle_4_deg	19.206
r_dihedral_angle_3_deg	17.655
r_dihedral_angle_1_deg	4.742
r_scangle_it	2.379
r_scbond_it	1.546
r_angle_refined_deg	1.301
r_mcangle_it	0.889
r_mcbond_it	0.521
r_nbtor_refined	0.283
r_symmetry_hbond_refined	0.217
r_symmetry_vdw_refined	0.215
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.203
r_metal_ion_refined	0.108
r_chiral_restr	0.091
r_symmetry_metal_ion_refined	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
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	3256
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	200

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction
MOLREP	phasing