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The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA12 tag inserted between the residues 181 and 186
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WKL 3wkl, 4yo0 experimental model PDB 4YO0 3wkl, 4yo0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 12-15%(wt./vol.) PEG 3350, 200mM sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.91 57.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.938 α = 90 b = 84.293 β = 90 c = 185.913 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 PILATUS3 S 6M 2018-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 48.23 100 0.056 0.94 12.6 6.7 54069
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 100 0.874 0.873 2.3 6.7
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 3wkl, 4yo0 2 48.23 51283 2701 99.97 0.215 0.21272 0.2138 0.2598 0.2616 RANDOM 47.625
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] 3.63 -0.26 -3.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.492 r_dihedral_angle_4_deg 15.107 r_dihedral_angle_3_deg 14.687 r_long_range_B_refined 6.964 r_dihedral_angle_1_deg 6.732 r_mcangle_it 3.803 r_scbond_it 3.329 r_mcbond_it 2.615 r_angle_refined_deg 1.108 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.492 r_dihedral_angle_4_deg 15.107 r_dihedral_angle_3_deg 14.687 r_long_range_B_refined 6.964 r_dihedral_angle_1_deg 6.732 r_mcangle_it 3.803 r_scbond_it 3.329 r_mcbond_it 2.615 r_angle_refined_deg 1.108 r_chiral_restr 0.08 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4725 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing