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X-ray structure of CorA N-terminal domain in complex with conformation-specific synthetic antibody C12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PGF experimental model PDB 2BBH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 293 8% dextrane sulfate, 17% PEG 3350, 0.02 M citric acid/0.08 M bis-Tris propane pH 8.8
Crystal Properties Matthews coefficient Solvent content 2.7 54.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.338 α = 90 b = 44.527 β = 108.01 c = 150.634 γ = 90
Symmetry Space Group I 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 EIGER2 X 16M 3.3 Undulator (Undulator A) 2015-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.038 45.82 99.4 0.056 0.078 0.054 13.1 3.5 55678
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.09 0.657 0.918 0.637
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 2.04 45.82 52871 2747 99.3 0.16826 0.16559 0.174 0.21785 0.2201 RANDOM 38.968
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] -0.99 -1.28 -0.34 1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.527 r_dihedral_angle_4_deg 18.494 r_dihedral_angle_3_deg 15.956 r_dihedral_angle_1_deg 7.702 r_long_range_B_refined 7.239 r_long_range_B_other 7.107 r_scangle_other 4.616 r_mcangle_it 3.009 r_mcangle_other 3.009 r_scbond_other 2.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.527 r_dihedral_angle_4_deg 18.494 r_dihedral_angle_3_deg 15.956 r_dihedral_angle_1_deg 7.702 r_long_range_B_refined 7.239 r_long_range_B_other 7.107 r_scangle_other 4.616 r_mcangle_it 3.009 r_mcangle_other 3.009 r_scbond_other 2.923 r_scbond_it 2.922 r_mcbond_it 2.066 r_mcbond_other 2.066 r_angle_refined_deg 1.817 r_angle_other_deg 1.385 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 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 5425 Nucleic Acid Atoms Solvent Atoms 585 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing