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Crystal structure of C-terminal domain of human galectin-8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YV8 PDB ENTRY 2YV8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 281 27.5% PEG 8000, 0.2M ammonium phosphate, 6.5% Ethylene Glycol, 0.1M Na Cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.78 55.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.105 α = 90 b = 73.148 β = 90 c = 179.214 γ = 90
Symmetry Space Group P 21 2 21
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 MAR scanner 345 mm plate 2007-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 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 3.006 50 88.9 0.219 5.49 14838 13191
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 3 3.11 67.1 0.413 3.8 1432
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 PDB ENTRY 2YV8 3.01 20 12427 666 88.86 0.23129 0.22814 0.2919 0.2551 RANDOM 31.865
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] -1.48 0.71 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.609 r_dihedral_angle_4_deg 20.45 r_dihedral_angle_3_deg 19.942 r_dihedral_angle_1_deg 6.108 r_angle_refined_deg 1.214 r_scangle_it 0.414 r_scbond_it 0.273 r_mcangle_it 0.131 r_chiral_restr 0.076 r_mcbond_it 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.609 r_dihedral_angle_4_deg 20.45 r_dihedral_angle_3_deg 19.942 r_dihedral_angle_1_deg 6.108 r_angle_refined_deg 1.214 r_scangle_it 0.414 r_scbond_it 0.273 r_mcangle_it 0.131 r_chiral_restr 0.076 r_mcbond_it 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4192 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling