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Naturally occurring mutation of Humna ABO(H) Galactosyltransferase in complex with UDP: GTB/M214T_UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LZ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 ADA, manganese chloride, ammonium sulfate, MPD, glycerol, PEG 4000,, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.28 46.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.6 α = 90 b = 149.49 β = 90 c = 79.24 γ = 90
Symmetry Space Group C 2 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 113 IMAGE PLATE RIGAKU RAXIS IV 2006-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 1.67 20 100 0.054 15.2 6.71 36659 36659
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 1.67 1.73 100 0.299 4.9 6.33
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 1lz7 1.67 20 34825 1834 99.96 0.17835 0.17617 0.173 0.22193 0.2199 RANDOM 22.584
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] -0.42 0.72 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.763 r_dihedral_angle_4_deg 18.813 r_dihedral_angle_3_deg 13.264 r_dihedral_angle_1_deg 6.571 r_scangle_it 4.612 r_scbond_it 3.118 r_mcangle_it 2.058 r_angle_refined_deg 1.852 r_mcbond_it 1.413 r_metal_ion_refined 0.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.763 r_dihedral_angle_4_deg 18.813 r_dihedral_angle_3_deg 13.264 r_dihedral_angle_1_deg 6.571 r_scangle_it 4.612 r_scbond_it 3.118 r_mcangle_it 2.058 r_angle_refined_deg 1.852 r_mcbond_it 1.413 r_metal_ion_refined 0.424 r_nbtor_refined 0.314 r_symmetry_hbond_refined 0.222 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.195 r_symmetry_vdw_refined 0.184 r_chiral_restr 0.139 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 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_other r_symmetry_vdw_other 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 2137 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling CCP4 phasing