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Crystal structure of the BiP NBD and MANF complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H9U 6H9U, 2W51 experimental model PDB 2W51 6H9U, 2W51
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 7% PEG6000, 0.1 M Tris-HCl pH7.5
Crystal Properties Matthews coefficient Solvent content 2.7 54.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.42 α = 81.13 b = 60.96 β = 88.33 c = 96.11 γ = 74.33
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2017-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.916 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.49 36.52 98.1 0.05 0.072 0.05 0.999 13.3 3.5 43348
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.49 2.55 98.1 0.707 0.999 0.707 0.617 1.6 3.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6H9U, 2W51 2.49 36.52 41261 2085 98.09 0.22782 0.22636 0.25608 0.2455 RANDOM 68.258
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] 1.67 -1.18 -0.53 -2.37 -0.55 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.83 r_dihedral_angle_4_deg 13.941 r_dihedral_angle_3_deg 13.654 r_dihedral_angle_1_deg 5.303 r_long_range_B_refined 2.061 r_long_range_B_other 2.061 r_mcangle_it 1.326 r_mcangle_other 1.326 r_scangle_other 1.175 r_angle_refined_deg 0.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.83 r_dihedral_angle_4_deg 13.941 r_dihedral_angle_3_deg 13.654 r_dihedral_angle_1_deg 5.303 r_long_range_B_refined 2.061 r_long_range_B_other 2.061 r_mcangle_it 1.326 r_mcangle_other 1.326 r_scangle_other 1.175 r_angle_refined_deg 0.794 r_mcbond_it 0.756 r_mcbond_other 0.756 r_angle_other_deg 0.686 r_scbond_it 0.665 r_scbond_other 0.665 r_chiral_restr 0.033 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 8214 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing