7OG0

Nontypeable Haemophillus influenzae SapA in open and closed conformations, in complex with double stranded RNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M8U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	22% (w/v) PEG 3350, 0.25 M NaBr, 0.1 M Bis-Tris Propane pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.26	α = 90
b = 147.97	β = 90
c = 59.55	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	PIXEL	DECTRIS PILATUS 6M		2014-08-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.920	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	2.61	65.74	97.4	0.078	0.102	0.995	8.27	3.8		38239			52.506

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.61	2.68	96.3		0.588	0.764	0.563	1.5	2.068

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	3M8U	2.61	65.74	36274	1870	96.87	0.1991	0.1965	0.2488	RANDOM	57.766

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]
-0.01			-0.61		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.985
r_dihedral_angle_4_deg	18.862
r_dihedral_angle_3_deg	16.322
r_dihedral_angle_1_deg	6.76
r_angle_refined_deg	1.175
r_angle_other_deg	0.854
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.985
r_dihedral_angle_4_deg	18.862
r_dihedral_angle_3_deg	16.322
r_dihedral_angle_1_deg	6.76
r_angle_refined_deg	1.175
r_angle_other_deg	0.854
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8009
Nucleic Acid Atoms	728
Solvent Atoms	157
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
xia2	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
Coot	model building
PHENIX	model building
XSCALE	data scaling
BALBES	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.