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Crystal structure of the p97-N/D1 hexamer in complex with six p47-UBX domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S3S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 14% PEG 3350, 0.2M ammonium citrate tribasic (pH 7), 0.01M hexamine cobalt (III) chloride
Crystal Properties Matthews coefficient Solvent content 3.25 62.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.78 α = 90 b = 178.85 β = 119.8 c = 171.33 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 ADSC QUANTUM 270 2010-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 2.7 40.013 99.3 0.038 0.999 9.4 7.4 242685
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 0.54 0.53
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 40.013 242656 11938 99.301 0.215 0.2132 0.2141 0.2558 0.2567 71.106
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] -0.821 0.114 4.489 -2.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.467 r_lrange_it 19.433 r_dihedral_angle_6_deg 15.777 r_scangle_it 14.595 r_dihedral_angle_1_deg 13.67 r_mcangle_it 12.298 r_scbond_it 10.028 r_mcbond_it 8.25 r_dihedral_angle_2_deg 5.722 r_angle_refined_deg 1.663
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.467 r_lrange_it 19.433 r_dihedral_angle_6_deg 15.777 r_scangle_it 14.595 r_dihedral_angle_1_deg 13.67 r_mcangle_it 12.298 r_scbond_it 10.028 r_mcbond_it 8.25 r_dihedral_angle_2_deg 5.722 r_angle_refined_deg 1.663 r_nbtor_refined 0.314 r_symmetry_xyhbond_nbd_refined 0.258 r_nbd_refined 0.252 r_symmetry_nbd_refined 0.168 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.126 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 48760 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 324
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling PHASER phasing