6QF5

X-Ray structure of human Aquaporin 2 crystallized on a silicon chip


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NEF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82950.1M Tris pH 8.5, 0.1M sodium chloride, 0.1M magnesium chloride, 22-25% PEG 400, cadmium chloride
Crystal Properties
Matthews coefficientSolvent content
3.4864.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.2α = 90
b = 122.2β = 90
c = 94.14γ = 90
Symmetry
Space GroupP 42

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELCS-PAD XPP2016-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.3670SLAC LCLSMFX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlSample Solvent
1on-chip crystallizationsingle crystalline silicon chipaluminum supportRoadrunner IInone, naked crystals
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
16019.07
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
13377137476

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (All)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
13.737.3899.970.7830.4372.3228.114866104.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.73.7699.930.1051.5380.9217.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4NEF3.733.8921.3314805148899.130.28730.28180.3357105.453
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.439
f_angle_d0.761
f_chiral_restr0.04
f_plane_restr0.007
f_bond_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6608
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms3

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHASERphasing
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling