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Crystal structure of nanobody D3-L11 mutant Y102A in complex with hen egg-white lysozyme (form II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293.15 20mM Tris-HCl pH 8.0, 100mM NaCl, 100mM LiCl, 18 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.16 43.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.01 α = 90 b = 49.44 β = 93.79 c = 57.94 γ = 90
Symmetry Space Group P 1 21 1
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 270 2015-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 1.55 49.44 99.7 0.094 0.996 10.8 5.1 36086
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 1.55 1.63 98 0.594 0.717 2.4 4.3
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 6JB2 1.55 49.44 34988 1083 99.61 0.13297 0.13182 0.1401 0.16856 0.1703 RANDOM 16.792
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] 0.63 0.49 -0.57 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.929 r_sphericity_free 21.438 r_dihedral_angle_4_deg 16.316 r_dihedral_angle_3_deg 12.479 r_dihedral_angle_1_deg 6.271 r_sphericity_bonded 6.049 r_long_range_B_refined 3.081 r_long_range_B_other 2.652 r_rigid_bond_restr 2.452 r_scangle_other 2.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.929 r_sphericity_free 21.438 r_dihedral_angle_4_deg 16.316 r_dihedral_angle_3_deg 12.479 r_dihedral_angle_1_deg 6.271 r_sphericity_bonded 6.049 r_long_range_B_refined 3.081 r_long_range_B_other 2.652 r_rigid_bond_restr 2.452 r_scangle_other 2.219 r_scbond_it 1.953 r_scbond_other 1.951 r_mcangle_other 1.774 r_mcangle_it 1.771 r_mcbond_it 1.589 r_angle_refined_deg 1.577 r_mcbond_other 1.575 r_angle_other_deg 1.032 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1955 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing