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)
TypeSourceAccession CodeDetails
experimental modelPDB 3M8U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29322% (w/v) PEG 3350, 0.25 M NaBr, 0.1 M Bis-Tris Propane pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.3848.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.26α = 90
b = 147.97β = 90
c = 59.55γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.920DiamondI04

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.6165.7497.40.0780.1020.9958.273.83823952.506
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)RedundancyNumber Unique Reflections (All)
12.612.6896.30.5880.7640.5631.52.068

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3M8U2.6165.7436274187096.870.19910.19650.2488RANDOM57.766
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]
-0.01-0.610.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.985
r_dihedral_angle_4_deg18.862
r_dihedral_angle_3_deg16.322
r_dihedral_angle_1_deg6.76
r_angle_refined_deg1.175
r_angle_other_deg0.854
r_chiral_restr0.062
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.985
r_dihedral_angle_4_deg18.862
r_dihedral_angle_3_deg16.322
r_dihedral_angle_1_deg6.76
r_angle_refined_deg1.175
r_angle_other_deg0.854
r_chiral_restr0.062
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8009
Nucleic Acid Atoms728
Solvent Atoms157
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
xia2data scaling
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
PHENIXmodel building
XSCALEdata scaling
BALBESphasing