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Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP-Glucose and glucose
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 6.5 293.15 2.0M Ammonium Sulphate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.43 49.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.415 α = 79.54 b = 46.59 β = 88.75 c = 69.904 γ = 75.83
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 RIGAKU RAXIS IV 2010-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 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 1.85 30.4 92.9 0.094 9.5 3.8 44258 44222 18.2
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 1.85 1.95 88.5 0.424 2.8 3.5 6135
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3Q4S 1.85 28.33 2 44222 42005 2217 92.84 0.19809 0.19506 0.25501 0.2625 RANDOM 24.652
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] 1.22 -1.66 0.83 0.28 0.99 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.435 r_dihedral_angle_4_deg 17.5 r_dihedral_angle_3_deg 12.924 r_dihedral_angle_1_deg 6.257 r_scangle_it 2.746 r_scbond_it 1.916 r_angle_refined_deg 1.62 r_mcangle_it 1.09 r_angle_other_deg 1.074 r_mcbond_it 0.641
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.435 r_dihedral_angle_4_deg 17.5 r_dihedral_angle_3_deg 12.924 r_dihedral_angle_1_deg 6.257 r_scangle_it 2.746 r_scbond_it 1.916 r_angle_refined_deg 1.62 r_mcangle_it 1.09 r_angle_other_deg 1.074 r_mcbond_it 0.641 r_mcbond_other 0.186 r_chiral_restr 0.12 r_bond_refined_d 0.015 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 4169 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 162
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling