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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 263 and 266
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 20% (wt./vol.) PEG 3350
200 mM ammonium citrate (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 3.22 61.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.86 α = 90 b = 171.86 β = 90 c = 118.016 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 EIGER X 4M 2017-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1000 Photon Factory BL-1A
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 4 48.64 99.9 0.186 0.996 12.2 13.5 7742
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 4 4.47 100 0.744 0.911 3.9 12.5
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 4 48.64 7344 398 99.86 0.21606 0.21297 0.2112 0.2735 0.2742 RANDOM 132.422
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] -1.78 -1.78 3.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.811 r_dihedral_angle_3_deg 14.987 r_dihedral_angle_4_deg 13.758 r_long_range_B_refined 9.449 r_mcangle_it 4.998 r_dihedral_angle_1_deg 4.972 r_mcbond_it 2.801 r_scbond_it 2.436 r_angle_refined_deg 0.687 r_chiral_restr 0.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.811 r_dihedral_angle_3_deg 14.987 r_dihedral_angle_4_deg 13.758 r_long_range_B_refined 9.449 r_mcangle_it 4.998 r_dihedral_angle_1_deg 4.972 r_mcbond_it 2.801 r_scbond_it 2.436 r_angle_refined_deg 0.687 r_chiral_restr 0.053 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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 4724 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing