☰ Navigation Tabs
Crystal Structure of Human Glycogenin-1 (GYG1) T83M mutant complexed with manganese and UDP-glucose
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 8 293.15 25% PEG smears (PEG 6k, 8k, 10k), 0.2M MgCl2, 10% glycerol, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.36 47.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.65 α = 90 b = 100.61 β = 90 c = 49.1 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 2010-10-26 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 1.93 29.85 100 0.097 10.7 4.5 21806 21806 25.5
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 1.93 2.03 100 0.728 2 4.4 3129
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 1.93 28.86 2 21806 20690 1116 99.98 0.18674 0.1841 0.1843 0.23735 0.2361 RANDOM 22.627
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] -0.61 -0.54 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.602 r_dihedral_angle_4_deg 16.575 r_dihedral_angle_3_deg 13.224 r_dihedral_angle_1_deg 6.947 r_sphericity_free 5.476 r_sphericity_bonded 5.33 r_scangle_it 3.478 r_scbond_it 2.292 r_mcangle_it 1.464 r_angle_refined_deg 1.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.602 r_dihedral_angle_4_deg 16.575 r_dihedral_angle_3_deg 13.224 r_dihedral_angle_1_deg 6.947 r_sphericity_free 5.476 r_sphericity_bonded 5.33 r_scangle_it 3.478 r_scbond_it 2.292 r_mcangle_it 1.464 r_angle_refined_deg 1.404 r_mcbond_it 0.84 r_angle_other_deg 0.823 r_mcbond_other 0.222 r_chiral_restr 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1954 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 86
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling