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Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP and 1'-deoxyglucose
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 7.5 293.15 1.4M tri-sodium citrate dihydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.7 α = 79.57 b = 46.86 β = 88.96 c = 69.7 γ = 77.25
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 2010-11-22 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 1.77 30.46 91.1 0.075 9.8 3.8 50333 50332 26.5
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 1.77 1.87 87.6 0.538 2.1 3.8 7098
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 1.77 30 2 50332 47790 2540 91.11 0.20002 0.19754 0.1973 0.24661 0.2425 RANDOM 26.973
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] 1.19 -1.78 0.6 0.78 0.75 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.885 r_dihedral_angle_4_deg 15.736 r_dihedral_angle_3_deg 13.663 r_dihedral_angle_1_deg 6.326 r_scangle_it 2.989 r_scbond_it 1.961 r_angle_refined_deg 1.553 r_mcangle_it 1.285 r_angle_other_deg 0.985 r_mcbond_it 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.885 r_dihedral_angle_4_deg 15.736 r_dihedral_angle_3_deg 13.663 r_dihedral_angle_1_deg 6.326 r_scangle_it 2.989 r_scbond_it 1.961 r_angle_refined_deg 1.553 r_mcangle_it 1.285 r_angle_other_deg 0.985 r_mcbond_it 0.75 r_mcbond_other 0.211 r_chiral_restr 0.091 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 4164 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 118
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling