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Structure of Myc3 N-terminal JAZ-binding domain [44-238] in complex with Jas motif of JAZ9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Myc3[44-238]
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2 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 coefficient Solvent content 2.63 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.745 α = 90 b = 85.745 β = 90 c = 59.983 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2013-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 50 100 0.057 23.7 12 18916 18916
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Myc3[44-238] 1.95 42.91 17936 17922 971 99.92 0.20149 0.19987 0.1987 0.2344 0.2366 RANDOM 50.08
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 -0.57 1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.533 r_dihedral_angle_3_deg 13.279 r_dihedral_angle_4_deg 12.392 r_long_range_B_refined 6.945 r_dihedral_angle_1_deg 4.993 r_mcangle_it 3.136 r_scbond_it 2.387 r_mcbond_it 1.965 r_angle_refined_deg 1.008 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.533 r_dihedral_angle_3_deg 13.279 r_dihedral_angle_4_deg 12.392 r_long_range_B_refined 6.945 r_dihedral_angle_1_deg 4.993 r_mcangle_it 3.136 r_scbond_it 2.387 r_mcbond_it 1.965 r_angle_refined_deg 1.008 r_chiral_restr 0.073 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1493 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms
Software Software Software Name Purpose MD2 data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling