2A3P | pdb_00002a3p

Structure of Desulfovibrio desulfuricans G20 tetraheme cytochrome with bound molybdate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A3M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	20% PEG 4000, 5% ethylene glycol, 0.2M ZnCl2, 0.1 M imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.92	36.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.16	α = 90
b = 43.7	β = 90
c = 57.887	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	173	IMAGE PLATE	RIGAKU RAXIS IV			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.2	30	96.5	0.097				5706

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	2.2	2.28		94.1	0.523

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	2A3M	2.3	27.13	4479	4479	482	98.51	0.19668	0.197	0.191	0.19	0.248	0.25	RANDOM	37.371

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			1.33		-2.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.083
r_dihedral_angle_3_deg	17.388
r_dihedral_angle_1_deg	5.792
r_scangle_it	4.006
r_dihedral_angle_4_deg	3.962
r_scbond_it	3.193
r_mcangle_it	2.572
r_angle_refined_deg	1.856
r_mcbond_it	1.628
r_nbtor_refined	0.275

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.083
r_dihedral_angle_3_deg	17.388
r_dihedral_angle_1_deg	5.792
r_scangle_it	4.006
r_dihedral_angle_4_deg	3.962
r_scbond_it	3.193
r_mcangle_it	2.572
r_angle_refined_deg	1.856
r_mcbond_it	1.628
r_nbtor_refined	0.275
r_symmetry_hbond_refined	0.235
r_symmetry_vdw_refined	0.196
r_nbd_refined	0.192
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	804
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	177

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 R01GM157729.