4I84 | pdb_00004i84

The crystal structure of the Haemophilus influenzae HxuA secretion domain involved in the two-partner secretion pathway

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ODL	PDB ENTRY 2ODL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.095M TRI SODIUM CITRATE pH 5.6, 5% GLYCEROL, 19% ISOPROPANOL, 12% PEG4000, 0.5M IMIDAZOLE pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.99	α = 90
b = 70.84	β = 98.1
c = 104.98	γ = 90

Symmetry
Space Group	P 1 21 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 315r		2011-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.98011	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.5	41.9				89861	89775	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.59

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2ODL	1.5	41.9	2	89815	85287	4489	100	0.16154	0.159	0.15	0.21027	0.2	RANDOM	20.866

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]
0.02		-0.08	0.01		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.003
r_dihedral_angle_4_deg	22.897
r_dihedral_angle_3_deg	13.643
r_scangle_it	9.217
r_dihedral_angle_1_deg	7.197
r_scbond_it	6.09
r_mcangle_it	4.246
r_rigid_bond_restr	3.186
r_mcbond_it	2.864
r_angle_refined_deg	2.236

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.003
r_dihedral_angle_4_deg	22.897
r_dihedral_angle_3_deg	13.643
r_scangle_it	9.217
r_dihedral_angle_1_deg	7.197
r_scbond_it	6.09
r_mcangle_it	4.246
r_rigid_bond_restr	3.186
r_mcbond_it	2.864
r_angle_refined_deg	2.236
r_chiral_restr	0.156
r_bond_refined_d	0.027
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4278
Nucleic Acid Atoms
Solvent Atoms	429
Heterogen Atoms

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

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.