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Nicotiana benthamiana alpha-galactosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UAS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.2 M LiSO4
0.1 M BIS-TRIS 5.5 pH
25 %w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.29 46.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.037 α = 90 b = 74.037 β = 90 c = 133.307 γ = 90
Symmetry Space Group P 41 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 EIGER X 4M CRL 2016-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 64.72 98.8 5.4 7.2 9569
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 64.72
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1uas 2.8 64.72 9060 486 98.59 0.21432 0.21058 0.28505 0.2437 RANDOM 3.809
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] 0.5 0.5 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.106 r_dihedral_angle_4_deg 18.221 r_dihedral_angle_3_deg 14.858 r_dihedral_angle_1_deg 7.307 r_angle_other_deg 2.102 r_angle_refined_deg 1.545 r_long_range_B_refined 1.223 r_long_range_B_other 1.219 r_mcangle_it 0.36 r_mcangle_other 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.106 r_dihedral_angle_4_deg 18.221 r_dihedral_angle_3_deg 14.858 r_dihedral_angle_1_deg 7.307 r_angle_other_deg 2.102 r_angle_refined_deg 1.545 r_long_range_B_refined 1.223 r_long_range_B_other 1.219 r_mcangle_it 0.36 r_mcangle_other 0.36 r_scangle_other 0.216 r_mcbond_it 0.191 r_mcbond_other 0.19 r_scbond_it 0.109 r_scbond_other 0.109 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2799 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing