4MJG

Crystal structure of a DUF4853 family protein (ACTODO_00621) from Actinomyces odontolyticus ATCC 17982 at 2.65 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	2.4M ammonium sulfate, 0.1M Bicine pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.08	α = 90
b = 97.08	β = 90
c = 105.044	γ = 120

Symmetry
Space Group	P 32 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	PIXEL	DECTRIS PILATUS 6M	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)	2013-08-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97941,0.97868	SSRL	BL11-1

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	2.65	44.544	88.9	0.061	9.2	3.2	15164	15164

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	2.65	2.72	95.3		0.811	0.811	0.9	3.2	1182

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	2.65	44.544	15135	768	88.7	0.2351	0.2336	0.2609	RANDOM	80.9114

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]
1.57	1.57		1.57		-5.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.549
r_dihedral_angle_3_deg	14.511
r_dihedral_angle_4_deg	13.451
r_mcangle_it	7.081
r_dihedral_angle_1_deg	6.079
r_mcbond_it	4.491
r_mcbond_other	4.487
r_angle_refined_deg	1.023
r_angle_other_deg	0.782
r_chiral_restr	0.059

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.549
r_dihedral_angle_3_deg	14.511
r_dihedral_angle_4_deg	13.451
r_mcangle_it	7.081
r_dihedral_angle_1_deg	6.079
r_mcbond_it	4.491
r_mcbond_other	4.487
r_angle_refined_deg	1.023
r_angle_other_deg	0.782
r_chiral_restr	0.059
r_bond_refined_d	0.005
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	2696
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	39

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	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 R01GM133198.