☰ Navigation Tabs
X-ray crystal structure of Xenopus laevis galectin-Ib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 34% PEG 3350, 0.1M MES, 0.2M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.21 α = 90 b = 35.32 β = 111.82 c = 58.51 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS VII 2013-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.68 18.92 94.8 0.046 14.3 4.04 13973 13973 31.8
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 1.68 1.74 91.4 0.344 2.9 4.04 1334
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 3WUC 1.68 18.92 13263 710 94.74 0.2 0.19716 0.2065 0.25329 0.2532 RANDOM 22.589
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] 0.92 -1.47 0.63 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.934 r_dihedral_angle_3_deg 16.342 r_dihedral_angle_4_deg 11.734 r_dihedral_angle_1_deg 7.559 r_long_range_B_refined 6.637 r_long_range_B_other 6.581 r_scangle_other 5.13 r_scbond_it 3.444 r_scbond_other 3.441 r_mcangle_it 2.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.934 r_dihedral_angle_3_deg 16.342 r_dihedral_angle_4_deg 11.734 r_dihedral_angle_1_deg 7.559 r_long_range_B_refined 6.637 r_long_range_B_other 6.581 r_scangle_other 5.13 r_scbond_it 3.444 r_scbond_other 3.441 r_mcangle_it 2.847 r_mcangle_other 2.845 r_angle_refined_deg 2.152 r_mcbond_it 2.076 r_mcbond_other 2.076 r_angle_other_deg 0.973 r_chiral_restr 0.16 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 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 1055 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 28
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling