2HJ1

Crystal structure of a 3D domain-swapped dimer of protein HI0395 from Haemophilus influenzae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	2.0 M Ammonium Sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.381	α = 90
b = 74.381	β = 90
c = 117.027	γ = 90

Symmetry
Space Group	P 43 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	ADSC QUANTUM 315		2006-04-15	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 4		2006-06-16	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.98	NSLS	X4A
2	SYNCHROTRON	NSLS BEAMLINE X29A	1.743	NSLS	X29A

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
1,2	2.1	50	97.3	0.065	0.069	16.2	9		19260			45.016

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	2.1	2.18	98		0.427	0.385	4.1	7.4	1872

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.1	25.31	23224	19244	987	97.45	0.216	0.216	0.215	0.231	RANDOM	46.317

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]
0.27			0.27		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.054
r_dihedral_angle_4_deg	23.38
r_dihedral_angle_3_deg	16.777
r_dihedral_angle_1_deg	13.882
r_scangle_it	4.528
r_scbond_it	2.924
r_mcangle_it	2.227
r_angle_refined_deg	1.799
r_mcbond_it	1.322
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.054
r_dihedral_angle_4_deg	23.38
r_dihedral_angle_3_deg	16.777
r_dihedral_angle_1_deg	13.882
r_scangle_it	4.528
r_scbond_it	2.924
r_mcangle_it	2.227
r_angle_refined_deg	1.799
r_mcbond_it	1.322
r_nbtor_refined	0.315
r_symmetry_hbond_refined	0.254
r_symmetry_vdw_refined	0.218
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.142
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1269
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	20

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building
DM	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.