2A3M

Structure of Desulfovibrio desulfuricans G20 tetraheme cytochrome (oxidized form)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	298	20% PEG 4000, 5% ethylene glycol, 0.2M ZnCl2, 0.1 M imidazole, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.67	α = 90
b = 43.876	β = 90
c = 57.729	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						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97856	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.5	50	98	0.06		6.4		18098

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.55		86.3	0.238		4.6

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 2CTH	1.5	34.96	16220	16220	1836	97.91	0.17714	0.177	0.175	0.195	RANDOM	16.389

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]
0.58			0.04		-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.923
r_dihedral_angle_3_deg	14.062
r_dihedral_angle_1_deg	5.028
r_scangle_it	3.845
r_scbond_it	2.607
r_mcangle_it	2.388
r_dihedral_angle_4_deg	1.978
r_mcbond_it	1.503
r_angle_refined_deg	1.218
r_nbd_refined	0.341

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.923
r_dihedral_angle_3_deg	14.062
r_dihedral_angle_1_deg	5.028
r_scangle_it	3.845
r_scbond_it	2.607
r_mcangle_it	2.388
r_dihedral_angle_4_deg	1.978
r_mcbond_it	1.503
r_angle_refined_deg	1.218
r_nbd_refined	0.341
r_nbtor_refined	0.282
r_symmetry_vdw_refined	0.152
r_symmetry_hbond_refined	0.093
r_xyhbond_nbd_refined	0.092
r_chiral_restr	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	804
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	172

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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 R01GM133198.