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Human Calcium and Integrin Binding Protein 2 (CIB2) Fusion to TMC1 CBD-1 domain at 2.4 Angstroms resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WU5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 25% (w/v) Polyethylene glycol 3350, 0.1 M Tris (pH 8.5), 0.2 M Magnesium chloride hexahydrate.
Crystal Properties Matthews coefficient Solvent content 2.17 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.065 α = 90 b = 121.849 β = 91.74 c = 62.208 γ = 90
Symmetry Space Group P 1 21 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 2021-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 2.4 50 99.4 0.124 0.134 0.052 0.98 7 6.3 18424
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 2.4 2.44 99.5 0.263 0.289 0.119 0.948 5.4
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 2.41 43.55 17492 908 99.08 0.20334 0.20133 0.2059 0.24223 0.2446 RANDOM 38.379
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] -1.03 0.49 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.833 r_dihedral_angle_2_deg 8.341 r_long_range_B_refined 6.418 r_long_range_B_other 6.418 r_dihedral_angle_1_deg 4.916 r_scangle_other 4.908 r_mcangle_other 3.767 r_mcangle_it 3.766 r_scbond_it 3.009 r_scbond_other 3.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.833 r_dihedral_angle_2_deg 8.341 r_long_range_B_refined 6.418 r_long_range_B_other 6.418 r_dihedral_angle_1_deg 4.916 r_scangle_other 4.908 r_mcangle_other 3.767 r_mcangle_it 3.766 r_scbond_it 3.009 r_scbond_other 3.009 r_mcbond_it 2.41 r_mcbond_other 2.409 r_angle_refined_deg 1.258 r_angle_other_deg 0.493 r_chiral_restr 0.069 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 3806 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHENIX phasing