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Crystal structure of human proteasome alpha7 tetradecamer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J2P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 24% PEG400, 100 mM Tris-HCl (pH 7.5), 0.2 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.45 49.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.481 α = 90 b = 132.481 β = 90 c = 444.563 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315 2013-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.00000 NSRRC BL13B1
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 3.75 50 97.1 0.081 16.3 4.9 41746 40504 -3
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 3.75 3.81 98.5 0.497 2.5 5
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 1J2P 3.75 20 38252 2039 96.53 0.21349 0.20945 0.2108 0.29107 0.289 RANDOM 152.993
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] 4.99 4.99 -9.99
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 28.356 r_long_range_B_refined 28.355 r_scangle_other 21.485 r_mcangle_other 20.892 r_mcangle_it 20.891 r_scbond_it 13.746 r_scbond_other 13.746 r_mcbond_it 13.594 r_mcbond_other 13.592 r_angle_refined_deg 1.225
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 28.356 r_long_range_B_refined 28.355 r_scangle_other 21.485 r_mcangle_other 20.892 r_mcangle_it 20.891 r_scbond_it 13.746 r_scbond_other 13.746 r_mcbond_it 13.594 r_mcbond_other 13.592 r_angle_refined_deg 1.225 r_angle_other_deg 0.935 r_chiral_restr 0.055 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.006 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26493 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALEPACK data reduction DENZO data scaling MOLREP phasing