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Crystal Structure of Human Glycogenin-1 (GYG1), apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LL3 pdb id 1LL3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.15 20% PEG smears (PEG 2000, 3350, 4000, 5000MME), 0.1M PIPES, pH 7.0, 0.1M MgCl2, 0.1M KCl, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.42 49.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.02 α = 90 b = 101.22 β = 90 c = 48.75 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 2010-12-04 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 30.04 97 0.094 12.2 4.4 19979 19954 25.8
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 94.9 0.699 2 4.4 2784
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 id 1LL3 1.98 29.17 2 19954 18959 1017 96.52 0.18146 0.17844 0.1823 0.23827 0.235 RANDOM 23.295
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] -0.59 -1.41 2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.693 r_dihedral_angle_4_deg 20.208 r_dihedral_angle_3_deg 13.344 r_dihedral_angle_1_deg 5.929 r_scangle_it 5.925 r_scbond_it 4.356 r_mcangle_it 2.676 r_mcbond_it 1.716 r_angle_refined_deg 1.462 r_angle_other_deg 1.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.693 r_dihedral_angle_4_deg 20.208 r_dihedral_angle_3_deg 13.344 r_dihedral_angle_1_deg 5.929 r_scangle_it 5.925 r_scbond_it 4.356 r_mcangle_it 2.676 r_mcbond_it 1.716 r_angle_refined_deg 1.462 r_angle_other_deg 1.013 r_mcbond_other 0.461 r_chiral_restr 0.092 r_bond_refined_d 0.015 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 1981 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 37
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling