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Structure of kappa-on-heavy (KoH) antibody Fab bound to the cardiac hormone marinobufagenin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YHY 4YHY, 5DQD, 4LRN, 1EEQ, 4WCY experimental model PDB 5DQD 4YHY, 5DQD, 4LRN, 1EEQ, 4WCY experimental model PDB 4LRN 4YHY, 5DQD, 4LRN, 1EEQ, 4WCY experimental model PDB 1EEQ 4YHY, 5DQD, 4LRN, 1EEQ, 4WCY experimental model PDB 4WCY 4YHY, 5DQD, 4LRN, 1EEQ, 4WCY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M citric acid; 0.8 M ammonium sulfate; pH 5.0
Crystal Properties Matthews coefficient Solvent content 3.74 67.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.483 α = 90 b = 128.483 β = 90 c = 333.335 γ = 90
Symmetry Space Group I 4 2 2
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 S 6M 2016-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.9798 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 3.6 100 91.9 0.298 0.32 0.111 5.5 8.4 15341 -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 3.6 3.66 93.4 1.118 1.215 0.452 0.539 7.9
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 4YHY, 5DQD, 4LRN, 1EEQ, 4WCY 3.6 47.44 14000 711 88.07 0.2364 0.2339 0.2339 0.2871 0.2838 RANDOM 92.198
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] -1.63 -1.63 3.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.01 r_dihedral_angle_4_deg 17.707 r_dihedral_angle_3_deg 15.483 r_dihedral_angle_1_deg 7.671 r_angle_refined_deg 1.39 r_angle_other_deg 1.215 r_mcangle_it 1.09 r_mcbond_it 0.605 r_mcbond_other 0.605 r_chiral_restr 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.01 r_dihedral_angle_4_deg 17.707 r_dihedral_angle_3_deg 15.483 r_dihedral_angle_1_deg 7.671 r_angle_refined_deg 1.39 r_angle_other_deg 1.215 r_mcangle_it 1.09 r_mcbond_it 0.605 r_mcbond_other 0.605 r_chiral_restr 0.06 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6475 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing