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Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and glucose or a glucal species
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 Li2(SO4), 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.29 α = 90 b = 80.18 β = 100.67 c = 69.53 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 2011-05-24 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 1.68 22.78 100 0.055 13.9 4 58119 58070 22.6
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 1.68 1.77 100 0.546 2.1 3.8 8458
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 1.68 22.585 2 58119 55123 2946 99.91 0.15876 0.15705 0.1626 0.19041 0.1922 RANDOM 18.672
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] -0.82 -0.72 1.43 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.656 r_dihedral_angle_4_deg 12.248 r_dihedral_angle_3_deg 11.885 r_dihedral_angle_1_deg 6.134 r_angle_refined_deg 1.499 r_angle_other_deg 0.974 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.656 r_dihedral_angle_4_deg 12.248 r_dihedral_angle_3_deg 11.885 r_dihedral_angle_1_deg 6.134 r_angle_refined_deg 1.499 r_angle_other_deg 0.974 r_chiral_restr 0.092 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 4067 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 105
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling