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p97 ND1-A232E in complex with VIMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KO8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 0.1 M Tris, pH 8, 6-7 % ethanol, 100 mM NaCl, 3.6-4.2 % MPD
Crystal Properties Matthews coefficient Solvent content 2.93 57.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.998 α = 90 b = 144.998 β = 90 c = 119.817 γ = 120
Symmetry Space Group P 6 2 2
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 RAYONIX MX300-HS 2015-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
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 2.79 50 98.3 22.8 4 18688
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 4KO8 2.79 125.57 17735 933 98.22 0.19609 0.1928 0.1905 0.25649 0.2414 RANDOM 124.393
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] 1.44 0.72 1.44 -4.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.924 r_dihedral_angle_3_deg 21.036 r_dihedral_angle_4_deg 20.111 r_long_range_B_refined 16.112 r_long_range_B_other 16.112 r_scangle_other 10.323 r_mcangle_other 9.677 r_mcangle_it 9.672 r_dihedral_angle_1_deg 7.605 r_scbond_it 6.521
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.924 r_dihedral_angle_3_deg 21.036 r_dihedral_angle_4_deg 20.111 r_long_range_B_refined 16.112 r_long_range_B_other 16.112 r_scangle_other 10.323 r_mcangle_other 9.677 r_mcangle_it 9.672 r_dihedral_angle_1_deg 7.605 r_scbond_it 6.521 r_scbond_other 6.52 r_mcbond_it 6.398 r_mcbond_other 6.348 r_angle_refined_deg 1.928 r_angle_other_deg 1.12 r_chiral_restr 0.09 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 3834 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing