4RS9

Structure of Myc3 N-terminal JAZ-binding domain [44-238] in complex with Jas motif of JAZ9


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherMyc3[44-238]

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.2 M magnesium chloride, 0.1 M Tris, pH 8.5, and 30% (w/v) polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6353.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.745α = 90
b = 85.745β = 90
c = 59.983γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.95501000.05723.7121891618916
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.06100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTMyc3[44-238]1.9542.91179361792297199.920.201490.199870.2344RANDOM50.08
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]
-0.57-0.57-0.571.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.533
r_dihedral_angle_3_deg13.279
r_dihedral_angle_4_deg12.392
r_long_range_B_refined6.945
r_dihedral_angle_1_deg4.993
r_mcangle_it3.136
r_scbond_it2.387
r_mcbond_it1.965
r_angle_refined_deg1.008
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.533
r_dihedral_angle_3_deg13.279
r_dihedral_angle_4_deg12.392
r_long_range_B_refined6.945
r_dihedral_angle_1_deg4.993
r_mcangle_it3.136
r_scbond_it2.387
r_mcbond_it1.965
r_angle_refined_deg1.008
r_chiral_restr0.073
r_bond_refined_d0.006
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1493
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms

Software

Software
Software NamePurpose
MD2data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling