3FOO

A Triangular Cytochrome b562 Superstructure Mediated by Ni Coordination - Monoclinic Form

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	25% PEG2000, 0.2 M NaCl, 0.1 M TRIS, 3.3 mM NiCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.339	α = 90
b = 107.396	β = 105.52
c = 102.051	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315	Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)	2008-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.97607	SSRL	BL9-1

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	2.4	98.533	97.2	0.096	0.096	6.464	2.7	56311	55485	2	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	2.4	2.53	97		0.552	0.552	1.3	2.6	8079

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		THROUGHOUT	PDB entry 2QLA	2.4	98.53	57214	55103	3980	96.31	0.213	0.213	0.209	0.268	RANDOM	41.455

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]
0.1		0.11	-0.15		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.25
r_dihedral_angle_3_deg	19.263
r_dihedral_angle_4_deg	13.467
r_dihedral_angle_1_deg	5.06
r_scangle_it	1.714
r_angle_refined_deg	1.246
r_scbond_it	1.142
r_mcangle_it	0.63
r_mcbond_it	0.37
r_nbtor_other	0.324
r_angle_other_deg	0.317
r_nbtor_refined	0.278
r_symmetry_vdw_refined	0.223
r_symmetry_hbond_refined	0.215
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.14
r_nbd_other	0.093
r_chiral_restr	0.075
r_mcbond_other	0.046
r_metal_ion_refined	0.018
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9648
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	756

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOLREP	phasing