☰ Navigation Tabs
Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP and maltotetraose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q4S PDB ENTRY 3Q4S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293.15 2.0M Ammonium Sulphate, 0.2M Na/K tartrate, 0.1M Na Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.48 50.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.765 α = 79.36 b = 46.844 β = 88.45 c = 69.848 γ = 77.2
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 QUANTUM 315 Kirkpatrick Baez bimorph mirror pair 2010-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.45 45.6 94.5 0.043 15.7 3.7 95225 95223 16.7
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 1.45 1.53 91.6 0.425 2.8 3.5 13479
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 3Q4S 1.45 41.2 2 95223 90447 4776 94.52 0.16533 0.16388 0.171 0.1933 0.1986 RANDOM 23.031
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] 1.01 -1.04 0.27 0.2 0.68 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.949 r_dihedral_angle_4_deg 13.856 r_dihedral_angle_3_deg 12.288 r_scangle_it 7.058 r_dihedral_angle_1_deg 6.106 r_scbond_it 4.962 r_mcangle_it 3.715 r_mcbond_it 2.315 r_angle_refined_deg 1.526 r_angle_other_deg 0.967
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.949 r_dihedral_angle_4_deg 13.856 r_dihedral_angle_3_deg 12.288 r_scangle_it 7.058 r_dihedral_angle_1_deg 6.106 r_scbond_it 4.962 r_mcangle_it 3.715 r_mcbond_it 2.315 r_angle_refined_deg 1.526 r_angle_other_deg 0.967 r_mcbond_other 0.674 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4149 Nucleic Acid Atoms Solvent Atoms 599 Heterogen Atoms 181
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling