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Structure of 3E9 antibody Fab bound to marinobufagenin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Ammonium sulfate, PEG 3350, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.3 46.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.92 α = 97.37 b = 67.69 β = 106.35 c = 71.986 γ = 107
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2015-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.9900 ALS 5.0.2
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 80 89.7 0.031 0.043 0.031 17.4 1.9 51985 -3
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 2.03 47.5 0.324 0.458 0.324 0.827 1.4 1.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4PUB 2 67.23 41801 2269 77.49 0.23098 0.22851 0.2299 0.2764 0.2805 RANDOM 31.349
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] 0.21 -0.47 0.03 -0.13 -0.23 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.119 r_dihedral_angle_4_deg 14.891 r_dihedral_angle_3_deg 13.153 r_dihedral_angle_1_deg 6.914 r_long_range_B_refined 5.216 r_long_range_B_other 5.136 r_angle_refined_deg 1.333 r_angle_other_deg 1.009 r_mcangle_it 0.679 r_mcangle_other 0.679
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.119 r_dihedral_angle_4_deg 14.891 r_dihedral_angle_3_deg 13.153 r_dihedral_angle_1_deg 6.914 r_long_range_B_refined 5.216 r_long_range_B_other 5.136 r_angle_refined_deg 1.333 r_angle_other_deg 1.009 r_mcangle_it 0.679 r_mcangle_other 0.679 r_scangle_other 0.576 r_mcbond_it 0.372 r_mcbond_other 0.372 r_scbond_it 0.316 r_scbond_other 0.316 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 6455 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing