6J20

Crystal structure of the human NK1 substance P receptor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE293100mM MES, pH 6.0-6.6, 25-35% PEG 400, 200-350mM ammonium tartrate dibasic
Crystal Properties
Matthews coefficientSolvent content
4.0869.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.512α = 90
b = 102.512β = 90
c = 156.962γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.650990.130.998.39.226005101.91
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.83600.990.5

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 REPLACEMENTTHROUGHOUT4GRV, 4U152.746.623622120199.80.2340.2330.26RANDOM114.89
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]
-9.1286-9.128618.2572
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion19.62
t_omega_torsion2.46
t_angle_deg1
t_bond_d0.009
t_improper_torsion
t_pseud_angle
t_gen_planes
t_it
t_nbd
t_incorr_chiral_ct
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion19.62
t_omega_torsion2.46
t_angle_deg1
t_bond_d0.009
t_improper_torsion
t_pseud_angle
t_gen_planes
t_it
t_nbd
t_incorr_chiral_ct
t_dihedral_angle_d
t_trig_c_planes
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3147
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms37

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing