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Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 E286A mutant bound to ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K1R PDB ENTRY 4K1R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.2M Ammonium Phosphate dibasic, 20%w/v PEG 3350, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.48 50.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.017 α = 90 b = 95.322 β = 90 c = 112.944 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate 2013-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.74 50 100 0.116 0.116 26.3 5.8 63915 63013 2.76 2.76
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 1.74 1.78 100
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4K1R 1.74 72.85 63908 59814 3198 98.59 0.19647 0.19493 0.22546 0.2383 RANDOM 25.735
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] 0.04 -0.11 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.035 r_dihedral_angle_3_deg 14.237 r_dihedral_angle_4_deg 12.464 r_dihedral_angle_1_deg 6.342 r_scbond_it 3.138 r_mcangle_it 3.062 r_mcbond_it 2.273 r_mcbond_other 2.273 r_angle_refined_deg 2.063 r_angle_other_deg 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.035 r_dihedral_angle_3_deg 14.237 r_dihedral_angle_4_deg 12.464 r_dihedral_angle_1_deg 6.342 r_scbond_it 3.138 r_mcangle_it 3.062 r_mcbond_it 2.273 r_mcbond_other 2.273 r_angle_refined_deg 2.063 r_angle_other_deg 0.89 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 4124 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MOLREP phasing PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 data collection