4ONT | pdb_00004ont

Ternary host recognition complex of complement factor H, C3d, and sialic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OXUPDB ENTRY 3OXU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92930.1 M Tris-HCl, pH 9.0, 8% w/v PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8657.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.459α = 112.5
b = 82.536β = 110.71
c = 85.752γ = 99.98
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2013-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.07SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.1546.0997.2912608871833
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2194.42.33

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3OXU2.1546.099126083737440897.310.17490.172340.170.222820.22RANDOM58.619
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]
-1.530.530.56-2.560.161.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.291
r_dihedral_angle_4_deg17.953
r_dihedral_angle_3_deg16.778
r_long_range_B_refined11.098
r_mcangle_it7.75
r_dihedral_angle_1_deg6.968
r_scbond_it6.745
r_mcbond_it5.604
r_angle_refined_deg1.527
r_chiral_restr0.108
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9807
Nucleic Acid Atoms
Solvent Atoms489
Heterogen Atoms171

Software

Software
Software NamePurpose
DA+data collection
CCP4model building
REFMACrefinement
XDSdata reduction
XDSdata scaling
CCP4phasing