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p97 ND1-L198W 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 8 288 0.1 M Tris, pH 8, 15 % ethanol, 100 mM NaCl, 7 % MPD
Crystal Properties Matthews coefficient Solvent content 3.7 66.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.772 α = 90 b = 153.772 β = 90 c = 240.641 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 MX300HE 2014-11-01 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 3.41 50 95.9 11.6 4 22714
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 3.41 49.268 21880 1135 96.97 0.2362 0.23328 0.2313 0.29394 0.2872 RANDOM 134.956
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] -1.22 -0.61 -1.22 3.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.154 r_dihedral_angle_4_deg 19.155 r_dihedral_angle_3_deg 18.22 r_long_range_B_refined 17.093 r_long_range_B_other 17.092 r_dihedral_angle_1_deg 12.903 r_scangle_other 11.268 r_mcangle_it 10.185 r_mcangle_other 10.185 r_scbond_it 6.461
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.154 r_dihedral_angle_4_deg 19.155 r_dihedral_angle_3_deg 18.22 r_long_range_B_refined 17.093 r_long_range_B_other 17.092 r_dihedral_angle_1_deg 12.903 r_scangle_other 11.268 r_mcangle_it 10.185 r_mcangle_other 10.185 r_scbond_it 6.461 r_scbond_other 6.46 r_mcbond_it 6.101 r_mcbond_other 6.101 r_angle_refined_deg 1.948 r_angle_other_deg 1.214 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.004 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 7780 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing