4NZK

Crystal structure of a DHHW family protein (EUBSIR_00411) from Eubacterium siraeum DSM 15702 at 1.49 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.20M Sodium Iodide, 20.0% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.125	α = 90
b = 102.125	β = 90
c = 123.311	γ = 120

Symmetry
Space Group	P 61 2 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	ADSC QUANTUM 315	KOHZU: Double Crystal Si(111)	2013-10-17	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.918401,0.979346,0.979261	ALS	8.2.1

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	1.49	29.481	100	0.11	12.5	10.3	62386	62386

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	1.49	1.53	100		0.015	1.482	0.5	10.3	4543

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	1.49	29.481	62267	3144	99.85	0.1264	0.1247	0.1577	RANDOM	19.684

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	0.28		0.28		-0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.809
r_sphericity_free	27.121
r_dihedral_angle_4_deg	12.663
r_dihedral_angle_3_deg	11.4
r_sphericity_bonded	9.651
r_dihedral_angle_1_deg	5.4
r_rigid_bond_restr	3.424
r_mcangle_it	2.6
r_mcbond_it	2.208
r_mcbond_other	2.202

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.809
r_sphericity_free	27.121
r_dihedral_angle_4_deg	12.663
r_dihedral_angle_3_deg	11.4
r_sphericity_bonded	9.651
r_dihedral_angle_1_deg	5.4
r_rigid_bond_restr	3.424
r_mcangle_it	2.6
r_mcbond_it	2.208
r_mcbond_other	2.202
r_angle_refined_deg	1.653
r_angle_other_deg	0.816
r_chiral_restr	0.101
r_bond_refined_d	0.012
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	2389
Nucleic Acid Atoms
Solvent Atoms	367
Heterogen Atoms	14

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

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.