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Crystal structure of SIAH1 SINA domain in complex with a USP19 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 298 SIAH1 AT 17.6 MG/ML WAS
MIXED WITH A TWO-FOLD EXCESS OF USP19 PEPTIDE ON ICE FOR
30 MIN. BEFORE SETTING UP FOR CRYSTALLIZATION. CRYSTALS
WERE GROWN AT 298K USING THE SITTING DROP METHOD BY
MIXING 0.5 UL PROTEIN:PEPTIDE MIX WITH 0.5 UL WELL SOLUTION
CONSISTING OF 20% PEG6000, 0.1 M BICINE PH 9.0. THE
CRYSTALS WERE CRYOPROTECTED BY FIRST IMMERSION IN WELL
SOLUTION MIXED WITH 15% (FINAL) ETHYLENE GLYCOL, THEN
IMMERSION IN N-PARATONE.
Crystal Properties Matthews coefficient Solvent content 2.28 46.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.343 α = 90 b = 88.092 β = 103.24 c = 59.59 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315 2014-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
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 2.33 50 90.9 0.089 6.2 2.3 15818 67.92
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 2.33 2.37 58.9 0.44 1.5 513
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 4I7B 2.34 48.45 15802 780 89.68 0.2233 0.2218 0.2339 0.2512 0.2739 RANDOM 82.59
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] 4.7768 -1.8572 -19.3544 14.5776
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.94 t_omega_torsion 1.97 t_angle_deg 0.95 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.94 t_omega_torsion 1.97 t_angle_deg 0.95 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3079 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 4
Software Software Software Name Purpose HKL-3000 data reduction BUSTER-TNT refinement PDB_EXTRACT data extraction HKL-3000 data scaling MOLREP phasing