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Crystal structure of wild type alpha-1,3 Galactosyltransferase in the absence of ligands
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K4V PDB ENTRY 1K4V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.1M TRIS-HCL BUFFER PH 8.0 AND 1.4M AMMONIUM SULPHATE
Crystal Properties Matthews coefficient Solvent content 3.49 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.57 α = 90 b = 93.57 β = 90 c = 108.417 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 CCD ADSC CCD MIRRORS 2005-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 SRS PX14.1
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 2.57 50 98 0.07 24 18.7 15988
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 2.57 2.66 84.8 0.68 2.11 12
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 PDB ENTRY 1K4V 2.57 27.11 14566 1041 98.3 0.268 0.263 0.2493 0.328 0.3132 RANDOM 58.81
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] -0.06 -0.06 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.795 r_dihedral_angle_4_deg 22.493 r_dihedral_angle_3_deg 20.96 r_dihedral_angle_1_deg 7.456 r_scangle_it 2.371 r_angle_refined_deg 1.73 r_mcangle_it 1.577 r_scbond_it 1.516 r_mcbond_it 0.869 r_nbtor_refined 0.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.795 r_dihedral_angle_4_deg 22.493 r_dihedral_angle_3_deg 20.96 r_dihedral_angle_1_deg 7.456 r_scangle_it 2.371 r_angle_refined_deg 1.73 r_mcangle_it 1.577 r_scbond_it 1.516 r_mcbond_it 0.869 r_nbtor_refined 0.333 r_nbd_refined 0.25 r_symmetry_vdw_refined 0.248 r_xyhbond_nbd_refined 0.191 r_symmetry_hbond_refined 0.138 r_chiral_restr 0.118 r_bond_refined_d 0.02 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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_other r_long_range_B_refined 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 2300 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing