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Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP and maltohexaose
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 2.0M Ammonium Sulphate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.46 49.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.679 α = 79.56 b = 46.739 β = 88.71 c = 69.69 γ = 76.86
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 Q315 3x3 CCD Kirkpatrick Baez bimorph mirror pair 2010-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 1.5 45.45 94.9 0.043 11.4 2.4 85753 85751
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 1.5 1.58 92.2 0.362 2.4 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1.5 44.76 85753 81446 4306 94.92 0.18255 0.1807 0.1863 0.21743 0.2234 RANDOM 19.583
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] 0.55 -0.84 0.36 0.29 0.59 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.062 r_dihedral_angle_3_deg 11.768 r_dihedral_angle_4_deg 10.471 r_dihedral_angle_1_deg 5.852 r_angle_refined_deg 1.514 r_angle_other_deg 0.93 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.062 r_dihedral_angle_3_deg 11.768 r_dihedral_angle_4_deg 10.471 r_dihedral_angle_1_deg 5.852 r_angle_refined_deg 1.514 r_angle_other_deg 0.93 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4150 Nucleic Acid Atoms Solvent Atoms 608 Heterogen Atoms 242
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling