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Diploptera punctata inspired lipocalin-like Milk protein expressed in Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NYQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 15% of PEG MME 550, 100 mM MES pH 6.5, and 10 mM ZnSO4
Crystal Properties Matthews coefficient Solvent content 3.36 63.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.61 α = 90 b = 135.662 β = 90 c = 39.654 γ = 90
Symmetry Space Group P 21 21 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 PILATUS 6M 2019-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.35 20.612 100 0.073 0.998 18.1 12.7 12200
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 0.836 0.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4NYQ 2.35 20.6 12161 573 99.77 0.225 0.2222 0.2228 0.2782 0.2645 58.393
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] -2.572 1.942 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.272 r_dihedral_angle_4_deg 25.394 r_dihedral_angle_3_deg 18.236 r_dihedral_angle_1_deg 11.401 r_lrange_it 8.876 r_lrange_other 8.864 r_scangle_it 5.767 r_scangle_other 5.764 r_mcangle_it 4.793 r_mcangle_other 4.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.272 r_dihedral_angle_4_deg 25.394 r_dihedral_angle_3_deg 18.236 r_dihedral_angle_1_deg 11.401 r_lrange_it 8.876 r_lrange_other 8.864 r_scangle_it 5.767 r_scangle_other 5.764 r_mcangle_it 4.793 r_mcangle_other 4.79 r_scbond_it 3.519 r_scbond_other 3.517 r_mcbond_it 3.121 r_mcbond_other 3.112 r_angle_refined_deg 2.101 r_angle_other_deg 1.35 r_metal_ion_refined 0.302 r_symmetry_nbd_refined 0.283 r_nbd_refined 0.254 r_xyhbond_nbd_refined 0.211 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.187 r_nbd_other 0.183 r_symmetry_nbtor_other 0.093 r_chiral_restr 0.083 r_symmetry_metal_ion_refined 0.063 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1234 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 97
Software Software Software Name Purpose xia2 data reduction Aimless data scaling PHASER phasing PHENIX refinement Coot model building