3FA5

CRYSTAL STRUCTURE OF a DUF849 family protein (PDEN_3495) FROM PARACOCCUS DENITRIFICANS PD1222 AT 1.90 A RESOLUTION

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.314M magnesium chloride, 20.4% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.579	α = 90
b = 139.567	β = 90
c = 45.765	γ = 90

Symmetry
Space Group	P 21 21 2

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	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2008-10-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.94645,0.97967	APS	23-ID-B

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	1.9	29.501	90.8	0.136	0.136	4.467	5.2		43418			17.226

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	1.9	1.95	82.2		0.521	0.521	1.5	2.9	2851

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	1.9	29.501	43231	2222	90.3	0.207	0.205	0.248	RANDOM	22.746

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]
-1.18			-3.08		4.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.331
r_dihedral_angle_4_deg	19.498
r_dihedral_angle_3_deg	13.618
r_scangle_it	6.778
r_dihedral_angle_1_deg	5.876
r_scbond_it	5.135
r_mcangle_it	2.72
r_mcbond_it	1.818
r_angle_refined_deg	1.538
r_angle_other_deg	0.936

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.331
r_dihedral_angle_4_deg	19.498
r_dihedral_angle_3_deg	13.618
r_scangle_it	6.778
r_dihedral_angle_1_deg	5.876
r_scbond_it	5.135
r_mcangle_it	2.72
r_mcbond_it	1.818
r_angle_refined_deg	1.538
r_angle_other_deg	0.936
r_mcbond_other	0.727
r_chiral_restr	0.089
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4194
Nucleic Acid Atoms
Solvent Atoms	421
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
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 R01GM157729.