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Crystal structure of p97-N/D1 hexamer in complex with FAF1-UBX domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DYG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 0.2M sodium acetate, 0.1M sodium citrate (pH 5.6), 5% polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 2.87 57.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.665 α = 71.52 b = 134.484 β = 80.87 c = 148.223 γ = 87.53
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 210r 2009-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 3.1 48.8 97.4 0.088 0.998 7.7 3.9 150419
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.15 0.839 0.704 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.1 48.8 129500 6798 97.36 0.20016 0.19769 0.1995 0.24626 0.2482 RANDOM 91.028
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] 3.91 2.83 1.86 -0.14 1.64 -1.48
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 25.199 r_dihedral_angle_3_deg 21.19 r_dihedral_angle_2_deg 15.505 r_mcangle_it 14.991 r_scbond_it 12.089 r_mcbond_it 9.646 r_dihedral_angle_1_deg 5.993 r_angle_refined_deg 1.56 r_chiral_restr 0.109 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 25.199 r_dihedral_angle_3_deg 21.19 r_dihedral_angle_2_deg 15.505 r_mcangle_it 14.991 r_scbond_it 12.089 r_mcbond_it 9.646 r_dihedral_angle_1_deg 5.993 r_angle_refined_deg 1.56 r_chiral_restr 0.109 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 48411 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 324
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing