☰ Navigation Tabs
Structural insights into the interaction of p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 25% PEG 3350, BIS-TRIS PH 6.5, 0.2M
MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.03 39.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.802 α = 90 b = 74.402 β = 90 c = 222.114 γ = 90
Symmetry Space Group P 21 21 21
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 315r 2015-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.9796 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 50 98.9 9.1 10 34582
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.29
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 3QQ7 2.25 42.97 32415 1716 96.6 0.191 0.189 0.1961 0.23 0.2357 RANDOM 37.36
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] -0.02 0.04 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.697 r_dihedral_angle_4_deg 16.552 r_dihedral_angle_3_deg 14.357 r_long_range_B_refined 8.523 r_long_range_B_other 8.462 r_dihedral_angle_1_deg 6.435 r_scangle_other 6.032 r_mcangle_other 4.444 r_mcangle_it 4.443 r_scbond_it 3.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.697 r_dihedral_angle_4_deg 16.552 r_dihedral_angle_3_deg 14.357 r_long_range_B_refined 8.523 r_long_range_B_other 8.462 r_dihedral_angle_1_deg 6.435 r_scangle_other 6.032 r_mcangle_other 4.444 r_mcangle_it 4.443 r_scbond_it 3.86 r_scbond_other 3.859 r_mcbond_it 2.925 r_mcbond_other 2.924 r_angle_other_deg 1.797 r_angle_refined_deg 1.741 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_bond_other_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 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 5763 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction MOLREP data scaling