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Crystal structure of BiP ATPase domain in complex with CDNF C-terminal domain at 1.65 angstroms resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F0X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 100 mM HEPES pH 7.5, 200 mM NaCl, 25% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.522 α = 90 b = 80.612 β = 90 c = 102.349 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 PIXEL DECTRIS PILATUS3 6M 2022-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.999870 Diamond I24
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 1.65 40.31 99.2 0.108 0.123 0.058 0.995 8.1 4.3 50649
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 1.65 1.678 92.4 1.129 1.32 0.671 0.431 1.3 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.65 40.31 48172 2434 99.09 0.18161 0.18051 0.1924 0.2026 0.2135 RANDOM 26.25
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 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.953 r_dihedral_angle_2_deg 10.249 r_long_range_B_refined 6.145 r_long_range_B_other 6.072 r_dihedral_angle_1_deg 5.867 r_scangle_other 3.02 r_scbond_it 1.951 r_scbond_other 1.951 r_mcangle_it 1.884 r_mcangle_other 1.883
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.953 r_dihedral_angle_2_deg 10.249 r_long_range_B_refined 6.145 r_long_range_B_other 6.072 r_dihedral_angle_1_deg 5.867 r_scangle_other 3.02 r_scbond_it 1.951 r_scbond_other 1.951 r_mcangle_it 1.884 r_mcangle_other 1.883 r_angle_refined_deg 1.464 r_mcbond_it 1.14 r_mcbond_other 1.14 r_angle_other_deg 0.504 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3250 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing