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Structure of Archeabacterial 20S proteasome mutant D9S- PA26 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PMA PDB entry 1PMA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 273 0.1M Na-citrate/phosphate buffer, 0.2M Lithium Sulfate, 15% PEG-1000, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 3.4 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 254.874 α = 90 b = 127.512 β = 92.45 c = 181.182 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 4 2004-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.283 NSLS X25
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 1.9 20 97.4 0.063 0.063 10 5 442007
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 1.9 1.97 95.8 0.497 2.2
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 (All) 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 1PMA 1.9 47.3 442001 440656 1345 97.24 0.18196 0.18196 0.18185 0.1821 0.21624 0.2136 RANDOM 31.532
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.69 r_dihedral_angle_4_deg 14.903 r_dihedral_angle_3_deg 14.644 r_dihedral_angle_1_deg 5.807 r_scangle_it 3.898 r_scbond_it 2.472 r_mcangle_it 1.51 r_angle_refined_deg 1.271 r_mcbond_it 0.973 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.69 r_dihedral_angle_4_deg 14.903 r_dihedral_angle_3_deg 14.644 r_dihedral_angle_1_deg 5.807 r_scangle_it 3.898 r_scbond_it 2.472 r_mcangle_it 1.51 r_angle_refined_deg 1.271 r_mcbond_it 0.973 r_nbtor_refined 0.3 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.167 r_symmetry_vdw_refined 0.161 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 34692 Nucleic Acid Atoms Solvent Atoms 3470 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing