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Crystal Structure of Myc3[44-238] from Arabidopsis in complex with Jaz1 peptide [200-221]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RQW PDB entry 4RQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 The MYC3(44-238)-JAZ1 complex crystals were grown at 20 degree in sitting drops containing 0.2 ul of the purified complex proteins at a concentration of 15 mg/ml and 0.2 ul of well solution containing 3.5 M sodium formate. Crystals of about 80 um in length appeared in 2 days
Crystal Properties Matthews coefficient Solvent content 2.62 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.209 α = 90 b = 86.209 β = 90 c = 59.36 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 2015-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.078 APS 21-ID-D
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 0.049 29.7 12.2 18921 18921
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 100 0.952 2.6 12.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4RQW 1.95 50 17940 965 99.98 0.18518 0.18363 0.21712 0.2075 RANDOM 44.609
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] -1 -0.5 -1 3.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.033 r_dihedral_angle_4_deg 23.041 r_dihedral_angle_3_deg 15.298 r_long_range_B_refined 8.533 r_dihedral_angle_1_deg 5.207 r_mcangle_it 3.637 r_scbond_it 3.261 r_mcbond_it 2.29 r_angle_refined_deg 1.089 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.033 r_dihedral_angle_4_deg 23.041 r_dihedral_angle_3_deg 15.298 r_long_range_B_refined 8.533 r_dihedral_angle_1_deg 5.207 r_mcangle_it 3.637 r_scbond_it 3.261 r_mcbond_it 2.29 r_angle_refined_deg 1.089 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1522 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing