4U9E

Crystal structure of the Zn-directed tetramer of the engineered cyt cb562 variant, A104/57G AB3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BC5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	27% (+/-)-2-methyl-2,4-pentanediol 400 in 100 mM Bis-Tris (pH 6.5) with 0.2M CaCl2 and 20 mM ampicillin

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.313	α = 90
b = 92.213	β = 90
c = 98.599	γ = 90

Symmetry
Space Group	F 2 2 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		2014-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	0.98	SSRL	BL14-1

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	2.8	35.66	98.9	0.048	0.048	22.2	4.3		4159

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	2.8	8.86	98.9		0.048	0.168	22.2	4.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2BC5	2.8	35.66	4104	184	98.6	0.239	0.237	0.285	RANDOM	57

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]
0.89			-0.34		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.99
r_dihedral_angle_3_deg	14.974
r_dihedral_angle_4_deg	7.817
r_dihedral_angle_1_deg	3.489
r_mcangle_it	2.221
r_mcbond_other	1.221
r_mcbond_it	1.22
r_angle_refined_deg	0.906
r_angle_other_deg	0.714
r_chiral_restr	0.067
r_bond_refined_d	0.006
r_bond_other_d	0.006
r_gen_planes_refined	0.002
r_gen_planes_other	0.002
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	712
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALA	data scaling