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Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and UDP
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 8.5 293.15 25% PEG 3350, 0.2M Ammonium sulfate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.4 48.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.4 α = 90 b = 100.97 β = 90 c = 48.94 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE RIGAKU RAXIS IV 2011-01-22 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 2.26 29.97 99.7 0.093 10.7 3.9 13895 13862 38.7
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 2.26 2.38 99.1 0.605 2 3.9 1970
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 2.26 29.03 2 13862 13168 693 99.72 0.20201 0.19929 0.192 0.25588 0.2521 RANDOM 27.926
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] -0.39 -1.23 1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.429 r_dihedral_angle_4_deg 22.815 r_dihedral_angle_3_deg 13.704 r_dihedral_angle_1_deg 6.45 r_scangle_it 3.445 r_scbond_it 2.194 r_angle_refined_deg 1.487 r_mcangle_it 1.402 r_angle_other_deg 0.991 r_mcbond_it 0.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.429 r_dihedral_angle_4_deg 22.815 r_dihedral_angle_3_deg 13.704 r_dihedral_angle_1_deg 6.45 r_scangle_it 3.445 r_scbond_it 2.194 r_angle_refined_deg 1.487 r_mcangle_it 1.402 r_angle_other_deg 0.991 r_mcbond_it 0.746 r_mcbond_other 0.15 r_chiral_restr 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1972 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 46
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling