☰ Navigation Tabs
Crystal structure of alginate-binding protein AlgQ2 without calcium ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M sodium formic acid
0.1 M 1,3-bis tris[(hydroxymethyl)methylamino]propane (pH 8.5)
20% polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.09 41.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.873 α = 80.37 b = 60.824 β = 89.81 c = 87.228 γ = 88.17
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 MARRESEARCH 2017-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1 SPring-8 BL38B1
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 2.2 50 97.8 0.145 63.6 2.7 47003
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 2.2 2.24 97.9 0.362 2.6
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 1J1N 2.2 50 43789 2350 97.77 0.21324 0.21012 0.212 0.27081 0.2723 RANDOM 29.677
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] 1.52 -0.39 -1.06 0.99 3.47 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.372 r_dihedral_angle_3_deg 16.573 r_dihedral_angle_4_deg 16.363 r_dihedral_angle_1_deg 6.18 r_long_range_B_refined 5.56 r_mcangle_it 2.574 r_scbond_it 2.226 r_mcbond_it 1.684 r_angle_refined_deg 1.517 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.372 r_dihedral_angle_3_deg 16.573 r_dihedral_angle_4_deg 16.363 r_dihedral_angle_1_deg 6.18 r_long_range_B_refined 5.56 r_mcangle_it 2.574 r_scbond_it 2.226 r_mcbond_it 1.684 r_angle_refined_deg 1.517 r_chiral_restr 0.107 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7974 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing