3GYX

Crystal structure of adenylylsulfate reductase from Desulfovibrio gigas

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.4	291	2M ammonium sulfate, 0.1M Tris, 1M guanidine hydrochloride, 0.2M sodium chloride, pH7.4, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 199.629	α = 90
b = 199.629	β = 90
c = 317.422	γ = 120

Symmetry
Space Group	P 31 2 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		2007-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.0	NSRRC	BL13B1

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	3.1	30	92	0.102	0.081	13.63	4.3	132767	122146		3.64

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)
	3.1	3.21	93.9		0.41	0.446	3.64	4.2	12375

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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	PDB ENTRY 1JNR	3.2	30	5	112993	105084	5561	91.68	0.1949	0.19226	0.24497	RANDOM	45.365

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]
0.28	0.14		0.28		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.913
r_dihedral_angle_3_deg	18.123
r_dihedral_angle_4_deg	15.58
r_dihedral_angle_1_deg	5.23
r_angle_refined_deg	1.048
r_scangle_it	0.623
r_mcangle_it	0.406
r_scbond_it	0.394
r_nbtor_refined	0.301
r_mcbond_it	0.224

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.913
r_dihedral_angle_3_deg	18.123
r_dihedral_angle_4_deg	15.58
r_dihedral_angle_1_deg	5.23
r_angle_refined_deg	1.048
r_scangle_it	0.623
r_mcangle_it	0.406
r_scbond_it	0.394
r_nbtor_refined	0.301
r_mcbond_it	0.224
r_nbd_refined	0.186
r_symmetry_vdw_refined	0.156
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.08
r_symmetry_hbond_refined	0.078
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	39054
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	414

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.