☰ Navigation Tabs
Crystal structure of Glycogen Debranching enzyme TreX from Sulfolobus solfataricus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BF2 PDB ENTRY 1BF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 2.2M AMMONIUM PHOSPHATE, 0.1M TRIS-HCL (PH 8.5)
Crystal Properties Matthews coefficient Solvent content 2.94 57.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.077 α = 90 b = 136.077 β = 90 c = 173.545 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC CCD 2007-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A PAL/PLS 4A
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 3 50 99.8 0.07 10.3 14.5 51429
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 2.7 2.8 99.5 0.41 2.75 7.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1BF2 3 29.91 35743 1909 99.8 0.218 0.215 0.221 0.287 0.2878 RANDOM 67.66
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] -0.15 -0.07 -0.15 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.697 r_dihedral_angle_3_deg 18.584 r_dihedral_angle_4_deg 14.768 r_dihedral_angle_1_deg 6.268 r_scangle_it 2.439 r_scbond_it 1.534 r_angle_refined_deg 1.372 r_mcangle_it 1.325 r_mcbond_it 0.734 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.697 r_dihedral_angle_3_deg 18.584 r_dihedral_angle_4_deg 14.768 r_dihedral_angle_1_deg 6.268 r_scangle_it 2.439 r_scbond_it 1.534 r_angle_refined_deg 1.372 r_mcangle_it 1.325 r_mcbond_it 0.734 r_nbtor_refined 0.314 r_nbd_refined 0.229 r_symmetry_hbond_refined 0.2 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.101 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11154 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHASER phasing