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Crystal structure of yeast proteasome interacting protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VLD PDB ENTRY 3VLD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 8% PEG 3000, 0.2M potassium phosphate, 0.1M Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.28 45.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.801 α = 90 b = 91.893 β = 113.06 c = 78.949 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 Bruker DIP-6040 2008-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
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 2.4 72.64 100 0.064 15.5 3.8 40079 -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 2.4 2.44 99.4 0.319
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 3VLD 2.41 72.64 37978 2005 99.37 0.20937 0.20601 0.2044 0.27397 0.2693 RANDOM 36.822
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 0.23 -0.01 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.819 r_dihedral_angle_4_deg 14.733 r_dihedral_angle_3_deg 13.297 r_scangle_it 6.543 r_scbond_it 4.065 r_dihedral_angle_1_deg 3.711 r_mcangle_it 2.489 r_mcbond_it 1.327 r_angle_refined_deg 0.951 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.819 r_dihedral_angle_4_deg 14.733 r_dihedral_angle_3_deg 13.297 r_scangle_it 6.543 r_scbond_it 4.065 r_dihedral_angle_1_deg 3.711 r_mcangle_it 2.489 r_mcbond_it 1.327 r_angle_refined_deg 0.951 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7059 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms
Software Software Software Name Purpose MLPHARE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling