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Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and UDP, in a monoclinic closed form
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 20% PEG 3350, 0.2M MgCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.2 44.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.02 α = 90 b = 80.72 β = 100.92 c = 69.85 γ = 90
Symmetry Space Group P 1 21 1
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 2011-01-19 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 1.98 30.43 97.3 0.074 10.7 3.3 34716 34694 25.2
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 1.98 2.09 95.3 0.497 2.1 3.2 4921
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 1.98 29.16 2 34694 32947 1745 96.99 0.20632 0.20326 0.2046 0.26546 0.2653 RANDOM 34.106
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] -1.43 -2.48 2.61 -2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.521 r_dihedral_angle_4_deg 18.51 r_dihedral_angle_3_deg 15 r_dihedral_angle_1_deg 6.395 r_scangle_it 2.772 r_scbond_it 1.947 r_angle_refined_deg 1.487 r_mcangle_it 1.234 r_angle_other_deg 0.974 r_mcbond_it 0.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.521 r_dihedral_angle_4_deg 18.51 r_dihedral_angle_3_deg 15 r_dihedral_angle_1_deg 6.395 r_scangle_it 2.772 r_scbond_it 1.947 r_angle_refined_deg 1.487 r_mcangle_it 1.234 r_angle_other_deg 0.974 r_mcbond_it 0.701 r_mcbond_other 0.17 r_chiral_restr 0.089 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 4027 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 52
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling