6V2E

Crystal structure of the human CLR:RAMP2 extracellular domain heterodimer with bound high-affinity adrenomedullin S45R/K46L/S48G/Q50W variant


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.329320% PEG MME 5000, 0.1 M sodium HEPEs pH 8.2, 150 mM sodium formate, 3% (v/v) dimethyl sulfoxide
Crystal Properties
Matthews coefficientSolvent content
2.6152.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.017α = 90
b = 84.993β = 90
c = 123.064γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105CCDMARMOSAIC 300 mm CCD2018-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.9786APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (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
11.835099.60.0870.0930.0346.87.463239
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.831.8698.91.181.2740.4760.6316.9

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 REPLACEMENTTHROUGHOUT4RWF1.8336.9759946323599.440.15820.15650.1896RANDOM29.177
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]
0.39-0.09-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.677
r_dihedral_angle_4_deg16.806
r_dihedral_angle_3_deg13.746
r_dihedral_angle_1_deg6.271
r_angle_refined_deg1.53
r_angle_other_deg1.41
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.677
r_dihedral_angle_4_deg16.806
r_dihedral_angle_3_deg13.746
r_dihedral_angle_1_deg6.271
r_angle_refined_deg1.53
r_angle_other_deg1.41
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4529
Nucleic Acid Atoms
Solvent Atoms602
Heterogen Atoms33

Software

Software
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing