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Crystal structure of Ups1-Mdm35 complex with PA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YTW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES pH 7.5, 10% PEG 6000, 5% MPD
Crystal Properties Matthews coefficient Solvent content 3.2 61.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.642 α = 90 b = 154.67 β = 104.42 c = 99.012 γ = 90
Symmetry Space Group C 1 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 90 CCD ADSC QUANTUM 210r 2014-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 3.2 50 100 0.123 19.4 7.7 50582
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 3.2 3.26 100 2.5 7.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4YTW 3.2 43.23 47542 4772 94.7 0.251 0.251 0.251 0.3 0.3003 RANDOM 94.6
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] -7.37 -2.97 -13.71 21.08
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.8 c_scangle_it 2.76 c_mcangle_it 2.55 c_angle_deg 1.7 c_scbond_it 1.66 c_improper_angle_d 1.43 c_mcbond_it 1.42 c_bond_d 0.014 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.8 c_scangle_it 2.76 c_mcangle_it 2.55 c_angle_deg 1.7 c_scbond_it 1.66 c_improper_angle_d 1.43 c_mcbond_it 1.42 c_bond_d 0.014 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15012 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 72
Software Software Software Name Purpose CNS refinement HKL-2000 data collection PHENIX model building