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Crystal structure of nanobody D3-L11 mutant Y102A in complex with hen egg-white lysozyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293.15 20mM TRIS HCl, 100mM NaCl, 100mM Sodium nitrate, 16% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.17 43.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.04 α = 90 b = 49.4 β = 93.7 c = 58.02 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 1.5 33.97 97.8 0.085 0.996 11.9 5.3 39075
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 1.5 1.58 85 0.48 0.804 2.8 3.9
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 1ZVY 1.5 33.97 37892 1167 97.73 0.12608 0.12479 0.1334 0.16494 0.1714 RANDOM 16.993
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] 0.66 0.38 -0.56 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.118 r_sphericity_free 25.784 r_dihedral_angle_4_deg 16.869 r_dihedral_angle_3_deg 12.413 r_sphericity_bonded 9.124 r_dihedral_angle_1_deg 6.469 r_rigid_bond_restr 4.256 r_long_range_B_refined 3.973 r_long_range_B_other 3.748 r_scangle_other 3.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.118 r_sphericity_free 25.784 r_dihedral_angle_4_deg 16.869 r_dihedral_angle_3_deg 12.413 r_sphericity_bonded 9.124 r_dihedral_angle_1_deg 6.469 r_rigid_bond_restr 4.256 r_long_range_B_refined 3.973 r_long_range_B_other 3.748 r_scangle_other 3.523 r_scbond_other 3.085 r_scbond_it 3.084 r_mcangle_other 2.127 r_mcangle_it 2.126 r_mcbond_it 2.103 r_mcbond_other 2.08 r_angle_refined_deg 1.575 r_angle_other_deg 0.896 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 293 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing