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Crystal structure of Pyrococcus furiosus PbaA (monoclinic form), an archaeal homolog of proteasome-assembly chaperone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WZ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 30% MPD, 0.1 M sodium acetate (pH 4.6), and 20 mM calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.95 58.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.69 α = 90 b = 200.94 β = 110.96 c = 92.76 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 95 CCD ADSC QUANTUM 210 2011-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.55 50 99 0.043 0.999 17.5 3.8 101818
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.71 98.3 0.675 0.812 1.9 3.8
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 3WZ2 2.55 20 96609 5085 99 0.20939 0.20777 0.2136 0.24039 0.2444 RANDOM 83.267
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] 1.03 1.05 -3.45 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.377 r_dihedral_angle_3_deg 19.595 r_dihedral_angle_4_deg 17.85 r_long_range_B_refined 13.633 r_long_range_B_other 13.633 r_scangle_other 11.504 r_mcangle_it 9.292 r_mcangle_other 9.292 r_scbond_it 7.76 r_scbond_other 7.759
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.377 r_dihedral_angle_3_deg 19.595 r_dihedral_angle_4_deg 17.85 r_long_range_B_refined 13.633 r_long_range_B_other 13.633 r_scangle_other 11.504 r_mcangle_it 9.292 r_mcangle_other 9.292 r_scbond_it 7.76 r_scbond_other 7.759 r_mcbond_it 6.836 r_mcbond_other 6.836 r_dihedral_angle_1_deg 5.951 r_angle_refined_deg 1.549 r_angle_other_deg 0.952 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18670 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing