6TCE

Crystal structure of the GGCT site-bound MH1 domain of Smad5 containing a GGGS insertion in the Loop1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6FZS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP727721% PEG Smear Medium (PEG 2000, 3350, 4000, and 5000 MME), 0.05 M Hepes pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.8857.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.123α = 90
b = 106.123β = 90
c = 82.395γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.9253.0691.90.0460.0490.017121.17.94821
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)
12.923.0640.62.9983.2081.1290.3150.67.9

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 REPLACEMENTTHROUGHOUT6fzs2.9253482322789.80.21010.2080.2531RANDOM135.31
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]
-8.8465-8.846517.693
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion20.83
t_omega_torsion2.95
t_angle_deg0.97
t_bond_d0.01
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1000
Nucleic Acid Atoms328
Solvent Atoms
Heterogen Atoms1

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing