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Crystal structure of the BiP NBD and MANF SAP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.92 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.27 45.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.31 α = 90 b = 66.75 β = 106.54 c = 44.3 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M-F 2017-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 1.57 42.47 99.3 0.054 0.074 0.05 0.998 11.3 3.3 59404
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 1.57 1.61 99.8 0.86 1.165 0.781 0.52 3.3
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 3LDN 1.57 42.47 56543 2861 99.25 0.18542 0.18447 0.1928 0.20411 0.2135 RANDOM 25.081
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] 0.09 0.53 -1.2 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.181 r_dihedral_angle_3_deg 10.774 r_dihedral_angle_4_deg 10.46 r_dihedral_angle_1_deg 5.455 r_long_range_B_refined 4.307 r_long_range_B_other 4.092 r_scangle_other 2.362 r_mcangle_it 1.608 r_mcangle_other 1.607 r_scbond_other 1.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.181 r_dihedral_angle_3_deg 10.774 r_dihedral_angle_4_deg 10.46 r_dihedral_angle_1_deg 5.455 r_long_range_B_refined 4.307 r_long_range_B_other 4.092 r_scangle_other 2.362 r_mcangle_it 1.608 r_mcangle_other 1.607 r_scbond_other 1.439 r_scbond_it 1.438 r_angle_refined_deg 1.225 r_mcbond_it 0.977 r_mcbond_other 0.977 r_angle_other_deg 0.866 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 3231 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing