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Pholiota squarrosa lectin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XZK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.8 M potassium-sodium phosphate (pH 7.0), 5% 1,3-butanediol
Crystal Properties Matthews coefficient Solvent content 3.02 59.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.28 α = 90 b = 145.28 β = 90 c = 39.625 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r 2017-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 50 98.9 0.053 42.2 5.6 28520
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 0.391
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 5XZK 1.8 50 26967 1356 98.07 0.19826 0.19575 0.2042 0.24852 0.2561 RANDOM 33.655
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.597 r_dihedral_angle_3_deg 15.61 r_long_range_B_refined 7.823 r_long_range_B_other 7.806 r_dihedral_angle_1_deg 6.361 r_scangle_other 5.509 r_mcangle_other 4.786 r_mcangle_it 4.785 r_scbond_it 4.05 r_scbond_other 3.987
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.597 r_dihedral_angle_3_deg 15.61 r_long_range_B_refined 7.823 r_long_range_B_other 7.806 r_dihedral_angle_1_deg 6.361 r_scangle_other 5.509 r_mcangle_other 4.786 r_mcangle_it 4.785 r_scbond_it 4.05 r_scbond_other 3.987 r_mcbond_it 3.39 r_mcbond_other 3.372 r_angle_refined_deg 2.255 r_angle_other_deg 1.099 r_chiral_restr 0.125 r_bond_refined_d 0.031 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_dihedral_angle_4_deg 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1855 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing