5NM9

Crystal structure of the placozoa Trichoplax adhaerens Smad4-MH1 bound to the GGCGC site.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2774.8% PEG 4000, 0.1 M sodium acetate pH 4.6
Crystal Properties
Matthew coefficientSolvent content
2.4148.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.15α = 90
b = 76.98β = 90
c = 145.04γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.976250ESRFID23-1

Data Collection

Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.432.441000.84.8

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 REPLACEMENTTHROUGHOUT5MEY2.4329.461619078698.80.2220.2210.251RANDOM82.04
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]
-8.65961.76986.8898
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion22.82
t_omega_torsion2.76
t_angle_deg1.02
t_bond_d0.01
t_improper_torsion
t_pseud_angle
t_gen_planes
t_it
t_nbd
t_incorr_chiral_ct
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion22.82
t_omega_torsion2.76
t_angle_deg1.02
t_bond_d0.01
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 Atoms1897
Nucleic Acid Atoms738
Solvent Atoms19
Heterogen Atoms2

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing