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Crystal structure of MJF14-6-4-2 Fab fragment in complex with epitope peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZTO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 Sitting droplets were set up by mixing 1 ul of Fab fragments, 0.5 ul of peptide (1 mg/ml in 20 mM tris-HCl) and 1 ul crystallization buffer (24% PEG 6000, 0.1M Na-citrate pH 5.0).
Crystal Properties Matthews coefficient Solvent content 2.28 46.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.484 α = 90 b = 66.7 β = 90 c = 167.167 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 EIGER2 XE 16M 2023-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976254 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.712 83.58 94.3 0.208 8.5 13 37216
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.712 1.902 1.609
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 1.712 83.58 30930 1594 70.39 0.19704 0.19531 0.2037 0.23117 0.2363 RANDOM 22.835
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] -0.17 0.16 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.487 r_dihedral_angle_1_deg 7.655 r_dihedral_angle_2_deg 6.766 r_long_range_B_refined 4.702 r_long_range_B_other 4.651 r_scangle_other 3.266 r_mcangle_it 2.937 r_mcangle_other 2.936 r_scbond_it 2.189 r_scbond_other 2.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.487 r_dihedral_angle_1_deg 7.655 r_dihedral_angle_2_deg 6.766 r_long_range_B_refined 4.702 r_long_range_B_other 4.651 r_scangle_other 3.266 r_mcangle_it 2.937 r_mcangle_other 2.936 r_scbond_it 2.189 r_scbond_other 2.188 r_mcbond_it 1.936 r_mcbond_other 1.935 r_angle_refined_deg 1.361 r_angle_other_deg 0.477 r_chiral_restr 0.063 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 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 3211 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing