☰ Navigation Tabs
Crystal structure of the Dario rerio galectin-1-L2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M HEPES pH 7.5, 0.2 M Magnesium Chloride Hexahydrate, 30% (v/v) PolyethG 400
Crystal Properties Matthews coefficient Solvent content 2.32 47.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.438 α = 90 b = 40.438 β = 90 c = 303.639 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 100 CCD RIGAKU SATURN 944 2012-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5
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 35 99.2 0.046 33.5 3.5 18718
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 2.05 97.3 0.218 6.5 2.7
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 1GAN 2 34.81 17755 963 99.26 0.17726 0.17405 0.1847 0.23405 0.2347 RANDOM 29.813
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 0.5 1 -3.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.107 r_dihedral_angle_4_deg 17.958 r_dihedral_angle_3_deg 13.395 r_dihedral_angle_1_deg 7.818 r_long_range_B_refined 7.534 r_long_range_B_other 7.321 r_scangle_other 4.502 r_mcangle_it 3.494 r_mcangle_other 3.493 r_scbond_it 2.984
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.107 r_dihedral_angle_4_deg 17.958 r_dihedral_angle_3_deg 13.395 r_dihedral_angle_1_deg 7.818 r_long_range_B_refined 7.534 r_long_range_B_other 7.321 r_scangle_other 4.502 r_mcangle_it 3.494 r_mcangle_other 3.493 r_scbond_it 2.984 r_scbond_other 2.984 r_mcbond_it 2.412 r_mcbond_other 2.412 r_angle_refined_deg 1.852 r_angle_other_deg 1.263 r_bond_refined_d 0.113 r_chiral_restr 0.069 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2138 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing