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Crystal structure of alpha-1,3 galactosyltransferase (alpha3GT) in a complex with p-nitrophenyl-beta-galactoside (pNP-beta-Gal)
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 5% PEG 6000, 0.1M TRIS-HCL, PH 8.0 IN THE PRESENCE OF 10MM MNCL2 AND 10MM UDP
Crystal Properties Matthews coefficient Solvent content 2.9 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.146 α = 90 b = 94.222 β = 99.05 c = 94.465 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC CCD MIRRORS 2006-10-05 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 2.12 50 94.4 0.09 12.4 3.1 44578 22.9
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 2.12 2.2 80.7 0.22 5.14 3
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1K4V 2.12 25.29 40981 1077 94.6 0.16959 0.16865 0.1689 0.20582 RANDOM 18.96
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.23 r_dihedral_angle_4_deg 16.659 r_dihedral_angle_3_deg 13.525 r_dihedral_angle_1_deg 5.749 r_angle_other_deg 1.481 r_scangle_it 1.435 r_angle_refined_deg 1.001 r_scbond_it 0.885 r_mcangle_it 0.649 r_mcbond_it 0.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.23 r_dihedral_angle_4_deg 16.659 r_dihedral_angle_3_deg 13.525 r_dihedral_angle_1_deg 5.749 r_angle_other_deg 1.481 r_scangle_it 1.435 r_angle_refined_deg 1.001 r_scbond_it 0.885 r_mcangle_it 0.649 r_mcbond_it 0.372 r_nbtor_refined 0.303 r_xyhbond_nbd_refined 0.204 r_nbd_refined 0.172 r_symmetry_vdw_refined 0.124 r_symmetry_hbond_refined 0.084 r_chiral_restr 0.073 r_bond_other_d 0.015 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 4784 Nucleic Acid Atoms Solvent Atoms 549 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing