☰ Navigation Tabs
Crystal structure of archaeal 20S proteasome in complex with mutated P26 activator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YAR PDB ENTRY 1YAR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 294 pH 5.6, VAPOR DIFFUSION, PEG 1000, HANGING DROP, temperature 294K, Sodium Phosphate Citrate, LiSo4, Imidazole, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.87 57.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 254.701 α = 90 b = 126.099 β = 92 c = 180.393 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 100 CCD ADSC QUANTUM 315 2008-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25
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 2.9 30 92.9 0.117 9.6 2.9 126445
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) 2.9 3 82.2 0.517 2.7
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 PDB ENTRY 1YAR 2.9 19.86 114890 2328 93.01 0.21271 0.21213 0.2178 0.24126 0.2458 RANDOM 47.849
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] 0.14 0.1 -0.18 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.072 r_dihedral_angle_4_deg 17.96 r_dihedral_angle_3_deg 16.784 r_dihedral_angle_1_deg 6.416 r_scangle_it 2.889 r_scbond_it 1.622 r_angle_refined_deg 1.455 r_mcangle_it 1.083 r_angle_other_deg 0.983 r_mcbond_it 0.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.072 r_dihedral_angle_4_deg 17.96 r_dihedral_angle_3_deg 16.784 r_dihedral_angle_1_deg 6.416 r_scangle_it 2.889 r_scbond_it 1.622 r_angle_refined_deg 1.455 r_mcangle_it 1.083 r_angle_other_deg 0.983 r_mcbond_it 0.536 r_mcbond_other 0.101 r_chiral_restr 0.079 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 35056 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection