3M79 | pdb_00003m79

A tetrameric Zn-bound cytochrome cb562 complex with covalently and non-covalently stabilized interfaces crystallized in the presence of Cu(II) and Zn(II)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IQ6

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.547	α = 90
b = 78.068	β = 90
c = 178.339	γ = 90

Symmetry
Space Group	P 21 21 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	Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing)	2010-01-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.0	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.099	89.17	93.6	0.102	4	9.5	49272	49272

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.21	84.2		0.176	1.5	10.3	6358

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3IQ6	2.1	59.87	52736	49203	3566	93.3	0.23	0.225	0.222	0.22	0.271	0.27	RANDOM	27.461

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]
0.04			-0.05		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.287
r_dihedral_angle_3_deg	16.866
r_dihedral_angle_4_deg	16.043
r_dihedral_angle_1_deg	6.068
r_scangle_it	2.151
r_scbond_it	1.475
r_angle_refined_deg	1.095
r_mcangle_it	0.798
r_mcbond_it	0.44
r_nbtor_refined	0.278

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.287
r_dihedral_angle_3_deg	16.866
r_dihedral_angle_4_deg	16.043
r_dihedral_angle_1_deg	6.068
r_scangle_it	2.151
r_scbond_it	1.475
r_angle_refined_deg	1.095
r_mcangle_it	0.798
r_mcbond_it	0.44
r_nbtor_refined	0.278
r_symmetry_vdw_refined	0.275
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.177
r_symmetry_hbond_refined	0.12
r_metal_ion_refined	0.09
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6544
Nucleic Acid Atoms
Solvent Atoms	395
Heterogen Atoms	352

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.